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Found 1 Document (0.686 seconds)

BMRB: 17716

2LEL

Structure of Cu(I)Cu(II)-CopK from Cupriavidus metallidurans CH34

Authors

Hinds, M.G., Xiao, Z., Chong, L., Wedd, A.G.

Assembly

Cu(I)Cu(II)-CopK

Entity

1. Cu(I)Cu(II)-CopK (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
3. CU (non-polymer), 63.546 Da
4. HOH (non-polymer), 18.015 Da

Total weight

8424.55 Da

Max. entity weight

8279.443 Da

Source organism

Cupriavidus metallidurans CH34

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.5 %, Completeness: 77.2 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.2 % (664 of 860)	75.8 % (345 of 455)	76.8 % (251 of 327)	87.2 % (68 of 78)
Backbone	82.6 % (365 of 442)	80.3 % (126 of 157)	82.5 % (175 of 212)	87.7 % (64 of 73)
Sidechain	72.4 % (349 of 482)	73.5 % (219 of 298)	70.4 % (126 of 179)	80.0 % (4 of 5)
Aromatic	32.6 % (15 of 46)	47.8 % (11 of 23)	17.4 % (4 of 23)
Methyl	67.9 % (38 of 56)	67.9 % (19 of 28)	67.9 % (19 of 28)

1. Cu(I)Cu(II)-CopK

VDMSNVVKTY DLQDGSKVHV FKDGKMGMEN KFGKSMNMPE GKVMETRDGT KIIMKGNEIF RLDEALRKGH SEGG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	Cu(I)Cu(II)-CopK	natural abundance	1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.45 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.45 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2011-10-11

Citation

Molecular basis of the cooperative binding of Cu(I) and Cu(II) to the CopK protein from Cupriavidus metallidurans CH34
Ash, M., Chong, L., Maher, M.J., Hinds, M.G., Xiao, Z., Wedd, A.G.
Biochemistry (2011), 50, 9237-9247, PubMed 21936507 , DOI 10.1021/bi200841f , Abstract

Related entities 1. Cu(I)Cu(II)-CopK, : 1 : 7 : 6 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	Cu(I)Cu(II)-CopK	natural abundance	1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

11 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

12 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	Cu(I)Cu(II)-CopK	[U-100% 13C; U-100% 15N]	1.0 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17716_2lel.nef
Input source #2: Coordindates	2lel.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Distance (Å)
A:2:ASP:OD1	C:null:CU:CU	2.0
A:70:HIS:ND1	C:null:CU:CU	2.0
C:null:CU:CU	D:null:HOH:O	2.0
A:1:VAL:N	C:null:CU:CU	2.201
A:44:MET:SD	B:null:CU1:CU	2.3
A:38:MET:SD	B:null:CU1:CU	2.301
A:28:MET:SD	B:null:CU1:CU	2.311
A:54:MET:SD	B:null:CU1:CU	2.314

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CU	COPPER (II) ION	None
C	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_17716_2lel.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	670		90.5 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1454 (1)	noe	75.7 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	73 (73)	.	77.0 (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: 90.5%
- Total number of assignments
  - ¹³C chemical shifts: 252
  - ¹H chemical shifts: 350
  - ¹⁵N chemical shifts: 68
- 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)
46	THR	HG1	5.486

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	327	252	77.1
¹H chemical shifts	455	349	76.7
¹⁵N chemical shifts	81	68	84.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	148	126	85.1
¹H chemical shifts	157	128	81.5
¹⁵N chemical shifts	73	64	87.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	179	126	70.4
¹H chemical shifts	298	221	74.2
¹⁵N chemical shifts	8	4	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	35	25	71.4
¹H chemical shifts	35	25	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	23	4	17.4
¹H chemical shifts	23	11	47.8

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: 75.7%
- Total number of restraints: 1454
- Weight of restraints: 1.0 (1454)
- Potential type of restraints: square-well-parabolic (1454)
- Range of distance target values: 2.1, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    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: 77.0%
- Total number of restraints: 73
- Total number of restraints per polymer type: 73
- Weight of restraints: 1.0 (73)
- Potential type of restraints: square-well-parabolic (73)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords binding cooperativity, copper protein, copper resistance, copper transport, protein structure

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Found 1 Document (0.686 seconds)

BMRB: 17716

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Cu(I)Cu(II)-CopK, : 1 : 7 : 6 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail