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Found 1 Document (1.072 seconds)

BMRB: 16277

2KIJ

Solution structure of the Actuator domain of the copper-transporting ATPase ATP7A

Authors

Banci, L., Bertini, I., Cantini, F., Migliardi, M., Nushi, F., Natile, G., Rosato, A.

Assembly

ATP7A

Entity

1. ATP7A (polymer, Thiol state: all free), 119 monomers, 12434.05 Da Detail

SEALAKLISL QATEATIVTL DSDNILLSEE QVDVELVQRG DIIKVVPGGK FPVDGRVIEG HSMVDESLIT GEAMPVAKKP GSTVIAGSIN QNGSLLICAT HVGADTTLSQ IVKLVEEAQ

Formula weight

12434.05 Da

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.1 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.1 % (1260 of 1297)	97.0 % (642 of 662)	97.1 % (496 of 511)	98.4 % (122 of 124)
Backbone	98.6 % (696 of 706)	98.0 % (239 of 244)	99.1 % (344 of 347)	98.3 % (113 of 115)
Sidechain	96.0 % (672 of 700)	96.4 % (403 of 418)	95.2 % (260 of 273)	100.0 % (9 of 9)
Aromatic	38.9 % (7 of 18)	77.8 % (7 of 9)	0.0 % (0 of 9)
Methyl	99.5 % (183 of 184)	98.9 % (91 of 92)	100.0 % (92 of 92)

1. Actd

SEALAKLISL QATEATIVTL DSDNILLSEE QVDVELVQRG DIIKVVPGGK FPVDGRVIEG HSMVDESLIT GEAMPVAKKP GSTVIAGSIN QNGSLLICAT HVGADTTLSQ IVKLVEEAQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details not labeled sample

#	Name	Isotope labeling	Concentration
1	Actd	natural abundance	0.2-0.3 (±0.05) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	phosphate	natural abundance	50 mM
5	arginine	natural abundance	50 mM
6	glutamate	natural abundance	50 mM
7	DTT	natural abundance	1 mM

Sample #2

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

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

Sample #3

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

#	Name	Isotope labeling	Concentration
15	Actd	[U-15N]	0.2-0.3 (±0.05) mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	phosphate	natural abundance	50 mM
19	arginine	natural abundance	50 mM
20	glutamate	natural abundance	50 mM
21	DTT	natural abundance	1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.4 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.4 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.4 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.4 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.5 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 2KIJ, Strand ID: A Detail

Release date

2009-09-03

Citation

Solution structures of the actuator domain of ATP7A and ATP7B, the Menkes and Wilson disease proteins
Banci, L., Bertini, I., Cantini, F., Migliardi, M., Nushi, F., Natile, G., Rosato, A.
Biochemistry (2009), 48, 7849-7855, PubMed 19645496 , DOI 10.1021/bi901003k , Abstract

Related entities 1. ATP7A, : 1 : 3 : 123 entities Detail

Interaction partners 1. ATP7A, : 5 interactors Detail

More details for 5 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
15	Actd	[U-15N]	0.2-0.3 (±0.05) mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	phosphate	natural abundance	50 mM
19	arginine	natural abundance	50 mM
20	glutamate	natural abundance	50 mM
21	DTT	natural abundance	1 mM

2 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 7.0

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details not labeled sample

#	Name	Isotope labeling	Concentration
1	Actd	natural abundance	0.2-0.3 (±0.05) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	phosphate	natural abundance	50 mM
5	arginine	natural abundance	50 mM
6	glutamate	natural abundance	50 mM
7	DTT	natural abundance	1 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details not labeled sample

#	Name	Isotope labeling	Concentration
1	Actd	natural abundance	0.2-0.3 (±0.05) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	phosphate	natural abundance	50 mM
5	arginine	natural abundance	50 mM
6	glutamate	natural abundance	50 mM
7	DTT	natural abundance	1 mM

5 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

6 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
15	Actd	[U-15N]	0.2-0.3 (±0.05) mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	phosphate	natural abundance	50 mM
19	arginine	natural abundance	50 mM
20	glutamate	natural abundance	50 mM
21	DTT	natural abundance	1 mM

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 7.0

#	Name	Isotope labeling	Concentration
8	Actd	[U-13C; U-15N]	0.2-0.3 (±0.05) mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %
11	phosphate	natural abundance	50 mM
12	arginine	natural abundance	50 mM
13	glutamate	natural abundance	50 mM
14	DTT	natural abundance	1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16277_2kij.nef
Input source #2: Coordindates	2kij.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--------90-----
GSFTMSEALAKLISLQATEATIVTLDSDNILLSEEQVDVELVQRGDIIKVVPGGKFPVDGRVIEGHSMVDESLITGEAMPVAKKPGSTVIAGSINQNGSL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSFTMSEALAKLISLQATEATIVTLDSDNILLSEEQVDVELVQRGDIIKVVPGGKFPVDGRVIEGHSMVDESLITGEAMPVAKKPGSTVIAGSINQNGSL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--100-------110---------
LICATHVGADTTLSQIVKLVEEAQ
||||||||||||||||||||||||
LICATHVGADTTLSQIVKLVEEAQ
-------110-------120----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	124	0	0	100.0

Content subtype: combined_16277_2kij.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1264		96.0 (chain: A, length: 124)
1	Distance restraints	AMBER_distance_constraints_4	OK	2373 (1)	noe	98.4 (chain: A, length: 124)
1	Dihedral angle restraints	AMBER_dihedral_5	OK	125 (125)	.	68.5 (chain: A, length: 124)
2	Dihedral angle restraints	AMBER_dihedral_7	Warning	1 (1)	.	1.6 (chain: A, length: 124)
1	RDC restraints	AMBER_dipolar_coupling_2	OK	102 (102)	.	82.3 (chain: A, length: 124)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 96.0%
- Total number of assignments
  - ¹H chemical shifts: 648
  - ¹³C chemical shifts: 494
  - ¹⁵N chemical shifts: 122
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	689	648	94.0
¹³C chemical shifts	533	494	92.7
¹⁵N chemical shifts	131	122	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	255	241	94.5
¹³C chemical shifts	248	236	95.2
¹⁵N chemical shifts	120	113	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	434	407	93.8
¹³C chemical shifts	285	258	90.5
¹⁵N chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	93	96.9
¹³C chemical shifts	96	91	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	7	50.0
¹³C chemical shifts	14	0	0.0

Distance restraints

Saveframe: AMBER_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 98.4%
- Total number of restraints: 2373
- Weight of restraints: 1.0 (2373)
- Potential type of restraints: square-well-parabolic (2373)
- Range of distance target values: 2.35, 5.36 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 68.5%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_7
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 1.6%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

RDC restraints

Saveframe: AMBER_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 82.3%
- Total number of restraints: 102
- Potential type of restraints: square-well-parabolic (102)
- Range of observed RDC values: -13.7, 19.7 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Actuator, ATP7A, Menkes disease, NMR

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Found 1 Document (1.072 seconds)

BMRB: 16277

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ATP7A, : 1 : 3 : 123 entities Detail

Interaction partners 1. ATP7A, : 5 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail