BMRBj - BMREntryMaster

Found 1 Document (0.888 seconds)

BMRB: 15655

2K0Q

Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34

Authors

Bersch, B., Favier, A., Schanda, P., Coves, J., van Aelst, S., Vallaeys, T., Wattiez, R., Mergeay, M.

Assembly

CopK

Entity

1. CopK (polymer, Thiol state: not present), 74 monomers, 8279.443 × 2 Da Detail

VDMSNVVKTY DLQDGSKVHV FKDGKMGMEN KFGKSMNMPE GKVMETRDGT KIIMKGNEIF RLDEALRKGH SEGG

Total weight

16558.887 Da

Max. entity weight

8279.443 Da

Source organism

Cupriavidus metallidurans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, H_exch_rates, RDCs

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.3 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (828 of 860)	98.5 % (448 of 455)	92.7 % (303 of 327)	98.7 % (77 of 78)
Backbone	98.6 % (436 of 442)	98.1 % (154 of 157)	99.1 % (210 of 212)	98.6 % (72 of 73)
Sidechain	94.6 % (456 of 482)	98.7 % (294 of 298)	87.7 % (157 of 179)	100.0 % (5 of 5)
Aromatic	50.0 % (23 of 46)	95.7 % (22 of 23)	4.3 % (1 of 23)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. CopK

VDMSNVVKTY DLQDGSKVHV FKDGKMGMEN KFGKSMNMPE GKVMETRDGT KIIMKGNEIF RLDEALRKGH SEGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
1	CopK	[U-100% 13C; U-100% 15N]	1.5 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
5	CopK	[U-100% 15N]	1.5 (±0.2) mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	MES	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
9	CopK	natural abundance	1.5 (±0.2) mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	MES	natural abundance	50 mM
13	C12E5	natural abundance	5 %
14	hexanol	natural abundance	5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
15	CopK	natural abundance	1.5 (±0.2) mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	MES	natural abundance	50 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
19	CopK	[U-100% 15N]	0.5 (±0.05) mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %
22	MES	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K0Q, Strand ID: A Detail

Heteronucl. T₁

62 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

Heteronucl. T₂

63 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

Heteronucl. T_1ρ

65 T_1ρ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

Heteronucl. NOE

68 NOE values in 1 lists
Value type peak height, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

Heteronucl. T₁/T₂

61 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

¹H exchange rate

63 k_ex values in 1 lists
Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

RDC

133 RDC values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0 Detail

Release date

2008-05-21

Citation 1

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

Show more 1 citaion

Citation 2

Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34
Monchy, S., Benotmane, M.A., Wattiez, R., van Aelst, S., Auquier, V., Borremans, B., Mergeay, M., Taghavi, S., van der Lelie, D., Vallaeys, T.
Microbiology (2006), 152, 1765-1776, PubMed 16735739 , DOI 10.1099/mic.0.28593-0 , Abstract

Hide non-primary 1 citaion

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

  BMRB: 16408 released on 2010-03-11
    Title Cu(I)-bound CopK
  Swiss-Prot: Q58AD3 released on 2008-07-22
    Title COPK_RALME Entity Copper resistance protein K

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

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian DirectDrive - 600 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
5	CopK	[U-100% 15N]	1.5 (±0.2) mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	MES	natural abundance	50 mM

2 3D HNCACB

Instrument

Varian INOVA - 800 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
1	CopK	[U-100% 13C; U-100% 15N]	1.5 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	50 mM

3 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
1	CopK	[U-100% 13C; U-100% 15N]	1.5 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	50 mM

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
1	CopK	[U-100% 13C; U-100% 15N]	1.5 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	50 mM

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
1	CopK	[U-100% 13C; U-100% 15N]	1.5 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	50 mM

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz + cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
15	CopK	natural abundance	1.5 (±0.2) mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	MES	natural abundance	50 mM

7 3D HNCO-type

Instrument

Varian DirectDrive - 600 MHz + cryoprobe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
9	CopK	natural abundance	1.5 (±0.2) mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	MES	natural abundance	50 mM
13	C12E5	natural abundance	5 %
14	hexanol	natural abundance	5 %

8 relaxation

Instrument

Varian DirectDrive - 600 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
5	CopK	[U-100% 15N]	1.5 (±0.2) mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	MES	natural abundance	50 mM

9 3D 15N NOESY-HSQC

Instrument

Varian INOVA - 800 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
5	CopK	[U-100% 15N]	1.5 (±0.2) mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	MES	natural abundance	50 mM

10 2D-Sofast

Instrument

Varian INOVA - 800 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0

#	Name	Isotope labeling	Concentration
5	CopK	[U-100% 15N]	1.5 (±0.2) mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	MES	natural abundance	50 mM

11 relaxation

Instrument

Varian DirectDrive - 600 MHz + cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.0, Details pH 6.0 (all samples)

#	Name	Isotope labeling	Concentration
19	CopK	[U-100% 15N]	0.5 (±0.05) mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %
22	MES	natural abundance	50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15655_2k0q.nef
Input source #2: Coordindates	2k0q.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----
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_15655_2k0q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	859		100.0 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	841 (1)	noe	95.9 (chain: A, length: 74)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	2004 (1)	noe	97.3 (chain: A, length: 74)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	4 (1)	noe	6.8 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	58 (58)	.	56.8 (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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 480
  - ¹³C chemical shifts: 302
  - ¹⁵N chemical shifts: 77
- 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	5.86

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	455	448	98.5
¹³C chemical shifts	327	301	92.0
¹⁵N chemical shifts	81	77	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	156	99.4
¹³C chemical shifts	148	146	98.6
¹⁵N chemical shifts	73	72	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	292	98.0
¹³C chemical shifts	179	155	86.6
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	22	95.7
¹³C chemical shifts	23	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- 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: 840
- Weight of restraints: 1.0 (840)
- Potential type of restraints: square-well-parabolic (840)
- Range of distance target values: 2.1, 3.65 (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
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 97.3%
  - Total number of restraints: 2002
  - Weight of restraints: 1.0 (2002)
  - Potential type of restraints: square-well-parabolic (2002)
  - Range of distance target values: 2.1, 4.4 (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
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 6.8%
    - Total number of restraints: 4
    - Weight of restraints: 1.0 (4)
    - Potential type of restraints: square-well-parabolic (4)
    - Range of distance target values: 2.1, 3.4 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 56.8%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords copper, heavy metal resistance, open barrel

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.888 seconds)

BMRB: 15655

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

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. CopK, : 1 : 7 : 6 entities Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail