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- PDB-1k0v: Copper trafficking: the solution structure of Bacillus subtilis CopZ -

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Basic information

Entry
Database: PDB / ID: 1k0v
TitleCopper trafficking: the solution structure of Bacillus subtilis CopZ
ComponentsCopZ
KeywordsMETAL TRANSPORT / beta-alpha-beta-beta-alpha-beta
Function / homology
Function and homology information


copper ion transport / copper ion binding / cytoplasm
Similarity search - Function
Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone CopZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsBanci, L. / Bertini, I. / Del Conte, R. / Markey, J. / Ruiz-Duenas, F.J.
CitationJournal: Biochemistry / Year: 2001
Title: Copper trafficking: the solution structure of Bacillus subtilis CopZ.
Authors: Banci, L. / Bertini, I. / Del Conte, R. / Markey, J. / Ruiz-Duenas, F.J.
History
DepositionSep 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence The last four amino acid segment IEGR, corresponding to the FactorXa recognition site used ...Sequence The last four amino acid segment IEGR, corresponding to the FactorXa recognition site used to remove the histidine tag, was engineered at the C-terminus of the construct.
Remark 600HETEROGEN COPPER (I) IS COORDINATED BY CYS 13 AND CYS 16.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CopZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8662
Polymers7,8031
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30
Representative

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Components

#1: Protein CopZ / probable mercuric ion-binding protein yvgY


Mass: 7802.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CopZ is involved in the copper trafficking of Bacillus subtilis and it does bind copper(I) under reducing conditions
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bscopz / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: O32221
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D TOSCY-HSQC
1213D NOESY-HSQC
1313D HNHA
2422D TOSCY
2522D NOESY
1612D HSQC
NMR detailsText: The structure was determined using heteronuclear technique

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Sample preparation

Details
Solution-IDContentsSolvent system
1Sample 1: 2mM Copper (I) loaded-Bacillus subtilis CopZ, 15N labelled. DTT was used as reductant. Sample 2: 2mM Copper (I) loaded-Bacillus subtilis CopZ, not labelled. DTT was used as reductant.100mM phosphate buffer, 90%H2O, 10%D2O
22mM Copper (I) loaded Bacillus subtilis CopZ, not labelled. DTT was used as reductant.100mM phosphate buffer, 90%H2O, 10%D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 1 atm300 K
27.0 1 atm300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guenter et al. 1997structure solution
XwinNMR2.6collection
XEASY1.3.13Eccles et al. 1991data analysis
Amber5Pearlman et al. 1997refinement
MOLMOL2.4Koradi et al. 1996data analysis
CORMABorgias et al. 1989data analysis
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR ensembleConformers calculated total number: 30 / Conformers submitted total number: 30

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