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Found 1 Document (0.805 seconds)

BMRB: 15373

2JSP

The prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A. tumefaciens Ros DNA binding domain

Authors

Malgieri, G.

Assembly

Ros87

Entity

1. Ros87 polypeptide (polymer, Thiol state: all free), 87 monomers, 9934.276 Da Detail

AVNVEKQKPA VSVRKSVQDD HIVCLECGGS FKSLKRHLTT HHSMTPEEYR EKWDLPVDYP MVAPAYAEAR SRLAKEMGLG QRRKANR

2. ZN (non-polymer), 65.409 Da

Total weight

9999.686 Da

Max. entity weight

9934.276 Da

Source organism

Agrobacterium tumefaciens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 83.8 %, Completeness (bb): 92.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.8 % (854 of 1019)	80.3 % (432 of 538)	87.8 % (345 of 393)	87.5 % (77 of 88)
Backbone	92.2 % (472 of 512)	94.8 % (164 of 173)	90.7 % (233 of 257)	91.5 % (75 of 82)
Sidechain	77.8 % (459 of 590)	73.4 % (268 of 365)	86.3 % (189 of 219)	33.3 % (2 of 6)
Aromatic	74.2 % (46 of 62)	74.2 % (23 of 31)	73.3 % (22 of 30)	100.0 % (1 of 1)
Methyl	84.1 % (69 of 82)	87.8 % (36 of 41)	80.5 % (33 of 41)

1. Ros87 polypeptide

AVNVEKQKPA VSVRKSVQDD HIVCLECGGS FKSLKRHLTT HHSMTPEEYR EKWDLPVDYP MVAPAYAEAR SRLAKEMGLG QRRKANR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
9	Ros87	natural abundance	1 mM
10	Zinc ion		1 mM
11	phosphate buffer		20 mM
12	NaCl		0.2 M

LACS Plot; CA

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

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2008-03-12

Citation

The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain
Malgieri, G., Russo, L., Esposito, S., Baglivo, I., Zaccaro, L., Pedone, E.M., Di Blasio, B., Isernia, C., Pedone, P.V., Fattorusso, R.
Proc. Natl. Acad. Sci. U. S. A. (2007), 104, 17341-17346, PubMed 17956987 , DOI 10.1073/pnas.0706659104 , Abstract

Related entities 1. Ros87 polypeptide, : 1 : 1 : 1 : 6 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
9	Ros87	natural abundance	1 mM
10	Zinc ion		1 mM
11	phosphate buffer		20 mM
12	NaCl		0.2 M

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

6 3D CBCANH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

7 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

8 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

9 3D HNHA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

12 3D CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

13 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
1	Ros87	[U-100% 15N]	1 mM
2	Zinc ion		1 mM
3	phosphate buffer		20 mM
4	NaCl		0.2 M

14 2D 1H-1H TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
9	Ros87	natural abundance	1 mM
10	Zinc ion		1 mM
11	phosphate buffer		20 mM
12	NaCl		0.2 M

15 2D 1H-15N HSQC IPAP

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

16 2D 1H-15N HSQC IPAP

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM phosphate buffer (pH=6.8), 0.2 M NaCl

#	Name	Isotope labeling	Concentration
5	Ros87	[U-100% 13C; U-100% 15N]	1 mM
6	Zinc ion		1 mM
7	phosphate buffer		20 mM
8	NaCl		0.2 M

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15373_2jsp.nef
Input source #2: Coordindates	2jsp.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80-------
AVNVEKQKPAVSVRKSVQDDHIVCLECGGSFKSLKRHLTTHHSMTPEEYREKWDLPVDYPMVAPAYAEARSRLAKEMGLGQRRKANR
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AVNVEKQKPAVSVRKSVQDDHIVCLECGGSFKSLKRHLTTHHSMTPEEYREKWDLPVDYPMVAPAYAEARSRLAKEMGLGQRRKANR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_15373_2jsp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	855		97.7 (chain: A, length: 87)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1759 (1)	noe	92.0 (chain: A, length: 87)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	416 (394)	.	100.0 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 429
  - ¹⁵N chemical shifts: 85
  - ¹³C chemical shifts: 341
- 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)
21	HIS	ND1	183.14
21	HIS	NE2	212.07
37	HIS	ND1	173.82
37	HIS	NE2	215.24
41	HIS	ND1	229.02
41	HIS	NE2	177.27
42	HIS	ND1	173.08
42	HIS	NE2	214.54
49	TYR	HH	10.99

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	538	428	79.6
¹⁵N chemical shifts	96	77	80.2
¹³C chemical shifts	393	341	86.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	164	94.8
¹⁵N chemical shifts	82	75	91.5
¹³C chemical shifts	174	153	87.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	365	264	72.3
¹⁵N chemical shifts	14	2	14.3
¹³C chemical shifts	219	188	85.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	38	86.4
¹³C chemical shifts	44	35	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	23	74.2
¹⁵N chemical shifts	1	1	100.0
¹³C chemical shifts	30	22	73.3

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 92.0%
- Total number of restraints: 1758
- Weight of restraints: 1.0 (1758)
- Potential type of restraints: upper-bound-parabolic (1758)
- Range of distance target values: 2.4, 14.02 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 100.0%
- Total number of restraints: 394
- Total number of restraints per polymer type: 394
- Weight of restraints: 1.0 (394)
- Potential type of restraints: square-well-parabolic (394)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Agrobacterium tumefaciens, Cys2His2 zinc finger, DNA binding proteins, NMR spectroscopy, Ros protein, prokaryotic Cys2His2 zinc finger

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Found 1 Document (0.805 seconds)

BMRB: 15373

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Ros87 polypeptide, : 1 : 1 : 1 : 6 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail