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BMRB: 16408

2KM0

Cu(I)-bound CopK

Authors

Bersch, B.

Assembly

periplasmic CopK protein complex

Entity

1. periplasmic CopK protein (polymer, Thiol state: not present), 74 monomers, 8279.443 Da Detail

VDMSNVVKTY DLQDGSKVHV FKDGKMGMEN KFGKSMNMPE GKVMETRDGT KIIMKGNEIF RLDEALRKGH SEGG

2. CU1 (non-polymer), 63.546 Da

Total weight

8342.989 Da

Max. entity weight

8279.443 Da

Source organism

Cupriavidus metallidurans

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 92.4 %, Completeness (bb): 93.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (795 of 860)	95.8 % (436 of 455)	87.5 % (286 of 327)	93.6 % (73 of 78)
Backbone	93.7 % (414 of 442)	94.9 % (149 of 157)	92.9 % (197 of 212)	93.2 % (68 of 73)
Sidechain	92.1 % (444 of 482)	96.3 % (287 of 298)	84.9 % (152 of 179)	100.0 % (5 of 5)
Aromatic	50.0 % (23 of 46)	100.0 % (23 of 23)	0.0 % (0 of 23)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. periplasmic CopK protein

VDMSNVVKTY DLQDGSKVHV FKDGKMGMEN KFGKSMNMPE GKVMETRDGT KIIMKGNEIF RLDEALRKGH SEGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	periplasmic CopK protein	[U-100% 15N]	1 mM
2	CU1	natural abundance	0.95 mM
3	ammonium acetate	natural abundance	50 mM
4	sodium ascorbate	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

Sample #3

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
9	periplasmic CopK protein	natural abundance	1.5 mM
10	CU1	natural abundance	1.4 mM
11	ammonium acetate	natural abundance	50 mM
12	sodium ascorbate	natural abundance	14 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	ammonium chloride	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	ammonium chloride	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	ammonium chloride	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	ammonium chloride	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: 0.19 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KM0, Strand ID: A Detail

Release date

2010-03-11

Citation 1

CopK from Cupriavidus metallidurans CH34 binds Cu(I) in a tetrathioether site: characterization by X-ray absorption and NMR spectroscopy
Sarret, G., Favier, A., Coves, J., Hazemann, J., Mergeay, M., Bersch, B.
J. Am. Chem. Soc. (2010), 132, 3770-3777, PubMed 20192263 , DOI 10.1021/ja9083896 , Abstract

Show more 1 citaion

Citation 2

Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge
Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Coves, J., Mergeay, M., Wattiez, R.
J. Mol. Biol. (2008), 380, 386-403, PubMed 18533181 , DOI 10.1016/j.jmb.2008.05.017 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 15655 released on 2008-05-21
    Title Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34
  Swiss-Prot: Q58AD3 released on 2008-07-22
    Title COPK_RALME Entity Copper resistance protein K

Related entities 1. periplasmic CopK protein, : 1 : 7 : 6 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	periplasmic CopK protein	[U-100% 15N]	1 mM
2	CU1	natural abundance	0.95 mM
3	ammonium acetate	natural abundance	50 mM
4	sodium ascorbate	natural abundance	10 mM

2 3D 1H-15N NOESY

Instrument

Varian DirectDrive - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	periplasmic CopK protein	[U-100% 15N]	1 mM
2	CU1	natural abundance	0.95 mM
3	ammonium acetate	natural abundance	50 mM
4	sodium ascorbate	natural abundance	10 mM

3 3D 1H-13C NOESY

Instrument

Varian DirectDrive - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

4 2D 1H-1H NOESY

Instrument

Varian DirectDrive - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
9	periplasmic CopK protein	natural abundance	1.5 mM
10	CU1	natural abundance	1.4 mM
11	ammonium acetate	natural abundance	50 mM
12	sodium ascorbate	natural abundance	14 mM

5 3D HNCO

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

6 3D HNCACB

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

7 3D HN(COCA)CB

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

8 3D HNCA

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

9 3D C(CO)NH

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

10 3D HCCH-TOCSY

Instrument

Varian DirectDrive - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	periplasmic CopK protein	[U-100% 13C; U-100% 15N]	1.6 mM
6	CU1	natural abundance	1.5 mM
7	ammonium acetate	natural abundance	50 mM
8	sodium ascorbate	natural abundance	16 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16408_2km0.nef
Input source #2: Coordindates	2km0.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	Warning

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)
1:44:MET:SD	2:1:CU1:CU	unknown	unknown	n/a
1:38:MET:SD	2:1:CU1:CU	unknown	unknown	n/a
1:54:MET:SD	2:1:CU1:CU	unknown	unknown	n/a
1:28:MET:SD	2:1:CU1:CU	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CU1	COPPER (I) ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70----
VDMSNVVKTYDLQDGSKVHVFKDGKMGMENKFGKSMNMPEGKVMETRDGTKIIMKGNEIFRLDEALRKGHSEGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VDMSNVVKTYDLQDGSKVHVFKDGKMGMENKFGKSMNMPEGKVMETRDGTKIIMKGNEIFRLDEALRKGHSEGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_16408_2km0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	783		97.3 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1535 (1)	noe	95.9 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	78 (78)	.	83.8 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 432
  - ¹³C chemical shifts: 278
  - ¹⁵N chemical shifts: 73
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
50	THR	HG1	5.53

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	455	425	93.4
¹³C chemical shifts	327	278	85.0
¹⁵N chemical shifts	81	73	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	146	93.0
¹³C chemical shifts	148	130	87.8
¹⁵N chemical shifts	73	68	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	279	93.6
¹³C chemical shifts	179	148	82.7
¹⁵N chemical shifts	8	5	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	35	100.0
¹³C chemical shifts	35	35	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	23	100.0
¹³C chemical shifts	23	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 95.9%
- Total number of restraints: 1535
- Weight of restraints: 1.0 (1535)
- Potential type of restraints: square-well-parabolic (1535)
- Range of distance target values: 1.2, 3.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 83.8%
- Total number of restraints: 78
- Total number of restraints per polymer type: 78
- Weight of restraints: 1.0 (78)
- Potential type of restraints: square-well-parabolic (78)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords heavy metal resistance, periplasmic copper binding protein

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Found 1 Document (0.784 seconds)

BMRB: 16408

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. periplasmic CopK protein, : 1 : 7 : 6 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail