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Yorodumi- PDB-2qif: Crystal structure of a metallochaperone with a tetranuclear Cu(I)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qif | ||||||
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Title | Crystal structure of a metallochaperone with a tetranuclear Cu(I) cluster | ||||||
Components | Copper chaperone copZ | ||||||
Keywords | CHAPERONE / TETRANUCLEAR CU(I) CLUSTER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | West, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qif.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qif.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qif_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 2qif_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 2qif_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2qif_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/2qif ftp://data.pdbj.org/pub/pdb/validation_reports/qi/2qif | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A SINGLE COPY OF THE BIOLOGICAL UNIT |
-Components
-Protein , 1 types, 2 molecules AB
#1: 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 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å |
Detector | Type: 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 |
Radiation | Monochromator: 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 wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1191.22 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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