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- PDB-2lel: Structure of Cu(I)Cu(II)-CopK from Cupriavidus metallidurans CH34 -

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Basic information

Entry
Database: PDB / ID: 2lel
TitleStructure of Cu(I)Cu(II)-CopK from Cupriavidus metallidurans CH34
ComponentsCopper resistance protein K
KeywordsMETAL BINDING PROTEIN / copper protein / copper transport / copper resistance / binding cooperativity
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Copper resistance protein K / Copper resistance protein K / CopK superfamily / Copper resistance protein K / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / COPPER (I) ION / Copper resistance protein K
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsHinds, M.G. / Xiao, Z. / Chong, L.X. / Wedd, A.G.
CitationJournal: Biochemistry / Year: 2011
Title: Molecular basis of the cooperative binding of Cu(I) and Cu(II) to the CopK protein from Cupriavidus metallidurans CH34.
Authors: Ash, M.R. / Chong, L.X. / Maher, M.J. / Hinds, M.G. / Xiao, Z. / Wedd, A.G.
History
DepositionJun 16, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper resistance protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4223
Polymers8,2951
Non-polymers1272
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Copper resistance protein K


Mass: 8294.567 Da / Num. of mol.: 1 / Fragment: CopK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: copK, Rmet_6108 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q58AD3
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-13C HSQC
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY
11023D 1H-15N NOESY
11122D 1H-13C HSQC
11222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM Cu(I)Cu(II)-CopK-1, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-100% 13C; U-100% 15N] Cu(I)Cu(II)-CopK-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMCu(I)Cu(II)-CopK-11
1.0 mMCu(I)Cu(II)-CopK-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1292 / NOE intraresidue total count: 601 / NOE long range total count: 331 / NOE medium range total count: 145 / NOE sequential total count: 215 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.027 Å / Distance rms dev error: 0.001 Å

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