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BMRB: 18301

2LQB

Metal binding repeat 2 of the Wilson disease protein (ATP7B)

Authors

Nokhrin, S., Dolgova, N.V., Yu, C., Dmitriev, O.Y.

Assembly

MBD2

Entity

1. MBD2 (polymer, Thiol state: all free), 76 monomers, 8416.620 Da Detail

AGHMQEAVVK LRVEGMTCQS CVSSIEGKVR KLQGVVRVKV SLSNQEAVIT YQPYLIQPED LRDHVNDMGF EAAIKS

Formula weight

8416.62 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 80.0 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.0 % (698 of 872)	75.1 % (341 of 454)	85.4 % (287 of 336)	85.4 % (70 of 82)
Backbone	90.7 % (410 of 452)	89.7 % (139 of 155)	90.6 % (202 of 223)	93.2 % (69 of 74)
Sidechain	69.0 % (339 of 491)	65.9 % (197 of 299)	77.2 % (142 of 184)	0.0 % (0 of 8)
Aromatic	23.5 % (8 of 34)	47.1 % (8 of 17)	0.0 % (0 of 17)
Methyl	84.0 % (79 of 94)	78.7 % (37 of 47)	89.4 % (42 of 47)

1. MBD2

AGHMQEAVVK LRVEGMTCQS CVSSIEGKVR KLQGVVRVKV SLSNQEAVIT YQPYLIQPED LRDHVNDMGF EAAIKS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

LACS Plot; CA

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.43 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-06-30

Citation

Copper chaperone Atox1 interacts with the metal-binding domain of Wilson's disease protein in cisplatin detoxification
Dolgova, N.V., Nokhrin, S., Yu, C.H., George, G.N., Dmitriev, O.Y.
Biochem. J. (2013), 454, 147-156, PubMed 23751120 , DOI 10.1042/BJ20121656 , Abstract

Related entities 1. MBD2, : 1 : 2 : 311 entities Detail

Interaction partners 1. MBD2, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

5 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

11 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Tris-Cl	[U-2H]		50 mM
2	DSS	natural abundance		0.5 mM
3	sodium azide	natural abundance		0.05 mM
4	D2O	[U-2H]		5 %
5	TCEP (tris(2-carboxyethyl)phosphine)	natural abundance		5 mM
6	H2O	[U-2H]		95 %
7	MBD2	[U-2H]		0.9 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18301_2lqb.nef
Input source #2: Coordindates	2lqb.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------
AGHMQEAVVKLRVEGMTCQSCVSSIEGKVRKLQGVVRVKVSLSNQEAVITYQPYLIQPEDLRDHVNDMGFEAAIKS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGHMQEAVVKLRVEGMTCQSCVSSIEGKVRKLQGVVRVKVSLSNQEAVITYQPYLIQPEDLRDHVNDMGFEAAIKS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_18301_2lqb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	689		93.4 (chain: A, length: 76)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1181 (1)	noe	86.8 (chain: A, length: 76)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	130 (90)	.	93.4 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 93.4%
- Total number of assignments
  - ¹H chemical shifts: 339
  - ¹³C chemical shifts: 281
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 86.8%
- Total number of restraints: 1181
- Weight of restraints: 1.0 (1181)
- Potential type of restraints: upper-bound-parabolic (1181)
- Range of distance target values: 2.25, 5.5 (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: 76, Sequence coverage: 93.4%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ATP7B, copper binding, Wilson disease