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BMRB: 25376

2MWX

The RING Domain of human Promyelocytic Leukemia Protein (PML)

Authors

Huang, S., Chang, C., Fan, P., Guntert, P., Shih, H., Huang, T.

Assembly

RING Domain of human Promyelocytic Leukemia Protein (PML)

Entity

1. RING Domain of human Promyelocytic Leukemia Protein (PML), entity 1 (polymer, Thiol state: free and other bound), 56 monomers, 6109.099 Da Detail

EEEFQFLRCQ QCQAEAKCPK LLPCLHTLCS GCLEASGMQC PICQAPWPLG ADTPAL

2. RING Domain of human Promyelocytic Leukemia Protein (PML), entity ZN (non-polymer), 65.409 × 2 Da

Total weight

6239.917 Da

Max. entity weight

6109.099 Da

Entity Connection

metal coordination 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS9:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS12:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS32:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS29:SG	2:ZN1:ZN
5	metal coordination	sing	1:HIS26:NE2	2:ZN1:ZN
6	metal coordination	sing	1:CYS40:SG	2:ZN1:ZN
7	metal coordination	sing	1:CYS24:SG	2:ZN1:ZN
8	metal coordination	sing	1:CYS43:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.3 %, Completeness (bb): 82.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.3 % (546 of 633)	94.3 % (313 of 332)	72.1 % (176 of 244)	100.0 % (57 of 57)
Backbone	82.7 % (268 of 324)	98.2 % (107 of 109)	67.3 % (111 of 165)	100.0 % (50 of 50)
Sidechain	91.2 % (330 of 362)	92.4 % (206 of 223)	88.6 % (117 of 132)	100.0 % (7 of 7)
Aromatic	33.3 % (12 of 36)	33.3 % (6 of 18)	29.4 % (5 of 17)	100.0 % (1 of 1)
Methyl	96.2 % (50 of 52)	96.2 % (25 of 26)	96.2 % (25 of 26)

1. entity 1

EEEFQFLRCQ QCQAEAKCPK LLPCLHTLCS GCLEASGMQC PICQAPWPLG ADTPAL

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	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

Sample #2

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

#	Name	Isotope labeling	Concentration
6	entity_1	[U-99% 13C; U-99% 15N]	1 mM
7	TRIS	[U-98% 2H]	25 mM
8	sodium chloride	natural abundance	100 mM
9	TCEP	natural abundance	0.2 mM
10	zinc chloride	natural abundance	1 mM

LACS Plot; CA

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

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-08-18

Citation

The RING domain of human promyelocytic leukemia protein (PML)
Huang, S., Chang, C., Fan, P., Guntert, P., Shih, H., Huang, T.
J. Biomol. NMR (2015), 61, 173-180, PubMed 25627356 , DOI 10.1007/s10858-015-9901-3 , Abstract

Related entities 1. RING Domain of human Promyelocytic Leukemia Protein (PML), entity 1, : 1 : 3 : 1 : 35 entities Detail

Interaction partners 1. RING Domain of human Promyelocytic Leukemia Protein (PML), entity 1, : 78 interactors Detail

More details for 78 interactors identified by 50 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

2 2D 1H-13C HSQC

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

3 3D CBCA(CO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

4 3D HNCO

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

5 3D HNCA

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

6 3D HCCH-TOCSY

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

7 3D 1H-15N NOESY

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

8 3D 1H-15N TOCSY

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
6	entity_1	[U-99% 13C; U-99% 15N]	1 mM
7	TRIS	[U-98% 2H]	25 mM
8	sodium chloride	natural abundance	100 mM
9	TCEP	natural abundance	0.2 mM
10	zinc chloride	natural abundance	1 mM

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
6	entity_1	[U-99% 13C; U-99% 15N]	1 mM
7	TRIS	[U-98% 2H]	25 mM
8	sodium chloride	natural abundance	100 mM
9	TCEP	natural abundance	0.2 mM
10	zinc chloride	natural abundance	1 mM

11 2D (HB)CB(CGCD)HD

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

12 2D (HB)CB(CGCDCE)HE

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

13 3D H(CCO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

14 3D C(CO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25376_2mwx.nef
Input source #2: Coordindates	2mwx.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	Error

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)
1:32:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:29:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:26:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:40:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:43:CYS:SG	2:2: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	Distance restraints
B	2	ZN	ZINC ION	None

Sequence alignments

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

-50-------60--------70--------80--------90-------100----
EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGADTPAL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGADTPAL
--------10--------20--------30--------40--------50------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_25376_2mwx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	549		100.0 (chain: A, length: 56)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1050 (1)	noe	100.0 (chain: A, length: 56)
2	Distance restraints	DYANA/DIANA_distance_constraints_6	Error	27 (1)	undefined	14.3 (chain: A, length: 56), 50.0 (chain: B, length: 2)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	11 (1)	hbond	17.9 (chain: A, length: 56)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	66 (66)	.	85.7 (chain: A, length: 56)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_4	OK	31 (31)	.	55.4 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 319
  - ¹³C chemical shifts: 173
  - ¹⁵N chemical shifts: 57
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	332	318	95.8
¹³C chemical shifts	244	173	70.9
¹⁵N chemical shifts	58	57	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	108	99.1
¹³C chemical shifts	112	56	50.0
¹⁵N chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	223	210	94.2
¹³C chemical shifts	132	117	88.6
¹⁵N chemical shifts	8	7	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	25	92.6
¹³C chemical shifts	27	25	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	8	44.4
¹³C chemical shifts	17	5	29.4
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 1050
- Weight of restraints: 1.0 (1050)
- Potential type of restraints: upper-bound-parabolic (1050)
- Range of distance target values: 2.4, 6.0 (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: DYANA/DIANA_distance_constraints_6
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 14.3%
    - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 27
  - Weight of restraints: 1.0 (27)
  - Potential type of restraints: upper-bound-parabolic (27)
  - Range of distance target values: 2.4, 3.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 17.9%
    - Total number of restraints: 11
    - Weight of restraints: 1.0 (11)
    - Potential type of restraints: upper-bound-parabolic (11)
    - Range of distance target values: 2.22, 3.13 (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: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 85.7%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 55.4%
- Total number of restraints: 31
- Potential type of restraints: undefined (31)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords E3 ligase, PML, RING finger, TRIM19

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Found 1 Document (1.623 seconds)

BMRB: 25376

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RING Domain of human Promyelocytic Leukemia Protein (PML), entity 1, : 1 : 3 : 1 : 35 entities Detail

Interaction partners 1. RING Domain of human Promyelocytic Leukemia Protein (PML), entity 1, : 78 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 7 contents Detail