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- PDB-1p8g: The solution structure of apo CopZ from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1p8g
TitleThe solution structure of apo CopZ from Bacillus subtilis
Componentssimilar to mercuric transport protein
KeywordsCHAPERONE / M-X-C-X-X-C motif / beta-alpha-beta-beta-alpha-beta secondary structure / copper chaperone
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 ...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 chaperone CopZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Simulate annealing, torsion angle dynamics
AuthorsBanci, L. / Bertini, I. / Del Conte, R.
CitationJournal: Biochemistry / Year: 2003
Title: Solution Structure of Apo CopZ from Bacillus subtilis: Further Analysis of the Changes Associated with the Presence of Copper
Authors: Banci, L. / Bertini, I. / Del Conte, R.
History
DepositionMay 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: similar to mercuric transport protein


Theoretical massNumber of molelcules
Total (without water)7,8031
Polymers7,8031
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)30 / 30structure with the lowest energy target function
Representative

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Components

#1: Protein similar to mercuric transport protein / BsCopZ


Mass: 7802.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bscopz / Plasmid: pet21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O32221

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
2323D 15N-separated NOESY
1423D 15N HSQC TOSCY
15215N-HSQC
26215N-HSQC
172HNHA
182HNHB
NMR detailsText: The 500 MHz spectrometer is equipped with a cryo probe

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM apo-BsCopZ100 mM phosphate buffer pH 7.0, with 1 eq of DTT reductant and 10% D2O. All manipulations were performed under inert atmosphere.
22mM apo-BsCopZ labelled with 15N100 mM phosphate buffer pH 7.0, with 1 eq of DTT reductant and 10% D2O. All manipulations were performed under inert atmosphere.
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
171 atm300 K
271 atm298 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
XwinNMR3.1collection
XEASY1.3.13data analysis
CORMAdata analysis
Amber5refinement
MOLMOL2.4data analysis
GLOMSAdata analysis
RefinementMethod: Simulate annealing, torsion angle dynamics / Software ordinal: 1
Details: A total of 1639 upper distance limits (of which 1431 meaningful), 31 dihedral phi angle constraints and 48 psi angle constraints were measured and used in the structural calculations. 5 ...Details: A total of 1639 upper distance limits (of which 1431 meaningful), 31 dihedral phi angle constraints and 48 psi angle constraints were measured and used in the structural calculations. 5 stereospecific assignments were also obtained from the analysis of HNHB spectra and 11 through the program GLOMSA.
NMR ensembleConformer selection criteria: structure with the lowest energy target function
Conformers calculated total number: 30 / Conformers submitted total number: 30

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