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Found 1 Document (2.546 seconds)

BMRB: 18192

2LO3

Solution structure of Sgf73(59-102) zinc finger domain

Authors

Gao, X., Koehler, C., Bonnet, J., Devys, D., Kieffer, B.

Assembly

SGF73

Entity

1. sgf73 (polymer, Thiol state: free and other bound), 44 monomers, 4786.421 Da Detail

NPNAQLIEDP LDKPIQYRVC EKCGKPLALT AIVDHLENHC AGAS

2. ZINC ION (non-polymer), 1 monomers, 65.409 Da

Total weight

4851.83 Da

Max. entity weight

4786.421 Da

Entity Connection

covalent 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:CYS20:SG	2:ZN1:ZN
2	covalent	sing	1:CYS23:SG	2:ZN1:ZN
3	covalent	sing	1:HIS35:NE2	2:ZN1:ZN
4	covalent	sing	1:HIS39:ND1	2:ZN1:ZN

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.6 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.6 % (423 of 494)	82.9 % (214 of 258)	89.0 % (170 of 191)	86.7 % (39 of 45)
Backbone	94.1 % (241 of 256)	91.9 % (79 of 86)	95.4 % (124 of 130)	95.0 % (38 of 40)
Sidechain	76.4 % (214 of 280)	73.3 % (126 of 172)	84.5 % (87 of 103)	20.0 % (1 of 5)
Aromatic	18.8 % (3 of 16)	37.5 % (3 of 8)	0.0 % (0 of 8)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. sgf73

NPNAQLIEDP LDKPIQYRVC EKCGKPLALT AIVDHLENHC AGAS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sgf73	[U-98% 15N]	0.2 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.05 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	sgf73	[U-98% 15N]	0.2 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	0.05 mM
17	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.28 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LO3, Strand ID: A Detail

Heteronucl. T₁

33 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.0 Detail

Heteronucl. T₂

33 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.0 Detail

Heteronucl. NOE

33 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.0 Detail

Heteronucl. T₁/T₂

33 T₁/T₂ values in 1 lists
Field strength (¹H) 600.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.0 Detail

Release date

2012-03-22

Citation

DNA binding by Sgf11 protein affects histone H2B deubiquitination by Spt-Ada-Gcn5-acetyltransferase (SAGA)
Koehler, C., Gao, X., Bonnet, J., Devys, D., Kieffer, B.
J. Biol. Chem. (2014), 289, 8989-8999, PubMed 24509845 , DOI 10.1074/jbc.M113.500868 , Abstract

Related entities 1. sgf73, : 1 : 4 : 6 : 7 entities Detail

Interaction partners 1. sgf73, : 68 interactors Detail

More details for 68 interactors identified by 11 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sgf73	[U-98% 15N]	0.2 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.05 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sgf73	[U-98% 15N]	0.2 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.05 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sgf73	[U-98% 15N]	0.2 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.05 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	sgf73	[U-98% 15N]	0.2 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	0.05 mM
17	D2O	natural abundance	100 %

5 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	sgf73	[U-98% 15N]	0.2 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	0.05 mM
17	D2O	natural abundance	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	sgf73	[U-98% 15N]	0.2 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	0.05 mM
17	D2O	natural abundance	100 %

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

9 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

10 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

11 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

13 3D HNCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

14 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

15 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

16 2D 1H-15N HSQC R1 edited

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

17 2D 1H-15N HSQC R2 edited

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

18 2D 1H-15N heteronuclear NOE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	sgf73	[U-99% 13C; U-98% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	75 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	10 %
12	H2O	natural abundance	90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18192_2lo3.nef
Input source #2: Coordindates	2lo3.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:35:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:39:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:20:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40----
NPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGAS
||||||||||||||||||||||||||||||||||||||||||||
NPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGAS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_18192_2lo3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	437		100.0 (chain: A, length: 44)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	832 (1)	noe	100.0 (chain: A, length: 44)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	18 (1)	hbond	34.1 (chain: A, length: 44)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	72 (72)	.	93.2 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 218
  - ¹³C chemical shifts: 175
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
35	HIS	HD1	7.1472
35	HIS	ND1	218.4424
35	HIS	NE2	172.4578
39	HIS	ND1	194.4283
39	HIS	NE2	175.0535

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	258	217	84.1
¹³C chemical shifts	191	175	91.6
¹⁵N chemical shifts	46	40	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	83	96.5
¹³C chemical shifts	88	84	95.5
¹⁵N chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	172	134	77.9
¹³C chemical shifts	103	91	88.3
¹⁵N chemical shifts	6	1	16.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	26	26	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	3	37.5
¹³C chemical shifts	8	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
- Total number of restraints: 823
- Weight of restraints: 1.0 (823)
- Potential type of restraints: square-well-parabolic (823)
- Range of distance target values: 2.9, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 34.1%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Range of distance target values: 1.8, 2.6 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 93.2%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Deubiquitination, Saga complex, Transcription factor, Zinc-finger

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Found 1 Document (2.546 seconds)

BMRB: 18192

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. sgf73, : 1 : 4 : 6 : 7 entities Detail

Interaction partners 1. sgf73, : 68 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 5 contents Detail