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- PDB-2k0q: Solution structure of CopK, a periplasmic protein involved in cop... -

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Basic information

Entry
Database: PDB / ID: 2k0q
TitleSolution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34
ComponentsPutative uncharacterized protein copK
KeywordsMETAL BINDING PROTEIN / copper / heavy metal resistance / open barrel / Plasmid-ENCODED
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 resistance protein K
Similarity search - Component
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBersch, B. / Favier, A. / Schanda, P. / Coves, J. / van Aelst, S. / Vallaeys, T. / Wattiez, R. / Mergeay, M.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.
Authors: Bersch, B. / Favier, A. / Schanda, P. / van Aelst, S. / Vallaeys, T. / Coves, J. / Mergeay, M. / Wattiez, R.
#1: Journal: Microbiology / Year: 2006
Title: Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34.
Authors: Monchy, S. / Benotmane, M.A. / Wattiez, R. / van Aelst, S. / Auquier, V. / Borremans, B. / Mergeay, M. / Taghavi, S. / van der Lelie, D. / Vallaeys, T.
History
DepositionFeb 12, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein copK


Theoretical massNumber of molelcules
Total (without water)8,2951
Polymers8,2951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative uncharacterized protein copK


Mass: 8294.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Gene: copK / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AD3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D HN(CA)CB
1313D H(CCO)NH
1413D C(CO)NH
1513D (H)CCH-TOCSY
1642D 1H-1H NOESY
1733D HNCO-type
1833D HNCO-type
192relaxation
11023D 15N NOESY-HSQC
11122D-SOFAST
1125relaxation

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] CopK, 50 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-100% 15N] CopK, 50 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
31.5 mM CopK, 50 mM MES, 5 % C12E5, 5 % hexanol, 90% H2O/10% D2O90% H2O/10% D2O
41.5 mM CopK, 50 mM MES, 100% D2O100% D2O
50.5 mM [U-100% 15N] CopK, 50 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMCopK[U-100% 13C; U-100% 15N]1
55 MH2O1
50 mMMES1
1.5 mMCopK[U-100% 15N]2
55 MH2O2
50 mMMES2
1.5 mMCopK3
55 MH2O3
50 mMMES3
5 %C12E53
5 %hexanol3
1.5 mMCopK4
55 MD2O4
50 mMMES4
0.5 mMCopK[U-100% 15N]5
55 MH2O5
50 mMMES5
Sample conditionsIonic strength: 0.1 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian DirectDriveVarianDirect Drive6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B.A. et al.chemical shift assignment
NMRViewJohnson, B.A. et al.peak picking
NMRViewJohnson, B.A. et al.data analysis
NMRDrawDelaglio, F. et al.peak picking
NMRDrawDelaglio, F. et al.geometry optimization
TALOSCornilescu, G. et al.data analysis
TENSORDosset, P. et al.data analysis
ModuleDosset, P. et al.data analysis
CNSBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: ATNOS/CANDID interfaced to CNS, ARIA 1.2 with ATNOS/CANDID + dihedral (Talos) restraints, water refinement, ARIA 1.2 with ATNOS/CANDID, dihedral (Talos) and rdc restraints, water refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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