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- PDB-2qif: Crystal structure of a metallochaperone with a tetranuclear Cu(I)... -

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Basic information

Entry
Database: PDB / ID: 2qif
TitleCrystal structure of a metallochaperone with a tetranuclear Cu(I) cluster
ComponentsCopper chaperone copZ
KeywordsCHAPERONE / TETRANUCLEAR CU(I) CLUSTER
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
ACETATE ION / COPPER (I) ION / Copper chaperone CopZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWest, C. / Singleton, C. / Kihlken, M.A. / Le Brun, N.E. / Hemmings, A.M.
Citation
Journal: Biochemistry / Year: 2009
Title: A tetranuclear Cu(I) cluster in the metallochaperone protein CopZ.
Authors: Hearnshaw, S. / West, C. / Singleton, C. / Zhou, L. / Kihlken, M.A. / Strange, R.W. / Le Brun, N.E. / Hemmings, A.M.
#1: Journal: Biochem.J. / Year: 2002
Title: Copper-mediated dimerization of CopZ, a predicted copper chaperone from Bacillus subtilis
Authors: Kihlken, M.A. / Leech, A.P. / Le Brun, N.E.
History
DepositionJul 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Copper chaperone copZ
B: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,19710
Polymers14,6922
Non-polymers5048
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-65 kcal/mol
Surface area7650 Å2
MethodPISA
2
A: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6836
Polymers7,3461
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5134
Polymers7,3461
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)23.440, 74.692, 41.212
Angle α, β, γ (deg.)90.00, 101.55, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A SINGLE COPY OF THE BIOLOGICAL UNIT

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Copper chaperone copZ / Copper-ion-binding protein


Mass: 7346.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 1A1 / Gene: copZ, yvgY / Plasmid: pMKNC6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O32221

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Non-polymers , 5 types, 174 molecules

#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 277 K / Method: vapor batch / pH: 4.6
Details: Crystallization by vapour batch using 12 microL drops in Terasaki plates covered with a thin layer of silicone oil and equilibrated against 10 % (v/v) isopropanol (24 h) then 20% (v/v) ...Details: Crystallization by vapour batch using 12 microL drops in Terasaki plates covered with a thin layer of silicone oil and equilibrated against 10 % (v/v) isopropanol (24 h) then 20% (v/v) isopropanol for 4 days. 15% (v/v) glycerol added as cryoprotectant., pH 4.6, VAPOUR BATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2002
Details: mirror; vertical focusing, glancing angle 3.5 mrad, 7.0 Ang. cut off, 1.2m long silicon substrate, rhodium coated, distance from source 16m
RadiationMonochromator: Si 111 optimised for 0.979 or 1.2 wavelength, horizontally focusing, distance from source 18m
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 41550 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Χ2: 2.19 / Net I/σ(I): 25.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.4 / Num. unique all: 3783 / Rsym value: 0.45 / Χ2: 2.636 / % possible all: 84.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→10 Å / Num. parameters: 11523 / Num. restraintsaints: 14831
Isotropic thermal model: INDIVIDUAL ATOMIC ANISOTROPIC TEMPERATURE FACTOR REFINEMENT
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1073 -RANDOM
all0.1302 20281 --
obs0.1302 20281 95.9 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1191.22
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 19 166 1192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0258
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.072

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