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BMRB: 25098

2MRY

NMR solution structure of copper binding protein in the apo form

Authors

Fu, Y., Wu, H., Bruce, K., Giedroc, D.

Assembly

copper binding protein in the apo form

Entity

1. copper binding protein in the apo form (polymer, Thiol state: all free), 98 monomers, 10876.49 Da Detail

GAMGQKAQQK NGYQEIRVEV MGGYTPELIV LKKSVPARIV FDRKDPSPCL DQIVFPDFGV HANLPMGEEY VVEITPEQAG EFSFACGMNM MHGKMIVE

Formula weight

10876.49 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.9 %, Completeness: 77.7 %, Completeness (bb): 78.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.7 % (887 of 1142)	85.3 % (510 of 598)	65.8 % (292 of 444)	85.0 % (85 of 100)
Backbone	78.2 % (449 of 574)	92.0 % (183 of 199)	63.7 % (181 of 284)	93.4 % (85 of 91)
Sidechain	79.1 % (519 of 656)	82.0 % (327 of 399)	77.4 % (192 of 248)	0.0 % (0 of 9)
Aromatic	50.0 % (41 of 82)	90.2 % (37 of 41)	9.8 % (4 of 41)
Methyl	97.9 % (94 of 96)	97.9 % (47 of 48)	97.9 % (47 of 48)

1. entity

GAMGQKAQQK NGYQEIRVEV MGGYTPELIV LKKSVPARIV FDRKDPSPCL DQIVFPDFGV HANLPMGEEY VVEITPEQAG EFSFACGMNM MHGKMIVE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: 0.33 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.33 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 18 models in PDB: 2MRY, Strand ID: A Detail

Release date

2015-07-26

Citation

Characterization of the structure and dynamics of the copper chaperone CupA
Fu, Y., Wu, H., Bruce, K., Giedroc, D.
Not known

Related entities 1. copper binding protein in the apo form, : 1 : 1 : 24 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

2 2D 1H-15N HSQC

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

3 3D CBCA(CO)NH

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

4 3D CBCANH

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

5 3D HNCO

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

6 3D C(CO)NH

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

7 3D H(CCO)NH

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

8 3D HCCH-TOCSY

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

9 3D HCCH-COSY

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

10 3D HNHA

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

11 3D 1H-15N NOESY

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

12 3D 1H-13C NOESY

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		0.4 ~ 0.6 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	EDTA	natural abundance		5 mM
5	TCEP	natural abundance		5 mM
6	DSS	natural abundance		10 uM
7	sodium azide	natural abundance		0.02 %
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25098_2mry.nef
Input source #2: Coordindates	2mry.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

---30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
GAMGQKAQQKNGYQEIRVEVMGGYTPELIVLKKSVPARIVFDRKDPSPCLDQIVFPDFGVHANLPMGEEYVVEITPEQAGEFSFACGMNMMHGKMIVE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGQKAQQKNGYQEIRVEVMGGYTPELIVLKKSVPARIVFDRKDPSPCLDQIVFPDFGVHANLPMGEEYVVEITPEQAGEFSFACGMNMMHGKMIVE
--------10--------20--------30--------40--------50--------60--------70--------80--------90--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	98	0	0	100.0

Content subtype: combined_25098_2mry.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	848		94.9 (chain: A, length: 98)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2775 (1)	noe	93.9 (chain: A, length: 98)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	130 (130)	.	92.9 (chain: A, length: 98)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 94.9%
- Total number of assignments
  - ¹H chemical shifts: 495
  - ¹⁵N chemical shifts: 84
  - ¹³C chemical shifts: 269
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 93.9%
- Total number of restraints: 2775
- Weight of restraints: 1.0 (2775)
- Potential type of restraints: square-well-parabolic (2775)
- Range of distance target values: 1.2, 2.75 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 92.9%
- Total number of restraints: 130
- Total number of restraints per polymer type: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein apo form