+Open data
-Basic information
Entry | Database: PDB / ID: 3n7d | ||||||
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Title | Crystal structure of CopK bound to Cu(I) and Cu(II) | ||||||
Components | Copper resistance protein K | ||||||
Keywords | METAL BINDING PROTEIN / copper (I) bound / copper (II) bound / copper resistance / methionine rich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cupriavidus metallidurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.149 Å | ||||||
Authors | Ash, M.-R. / Maher, M.J. | ||||||
Citation | Journal: To be Published Title: Two new crystal forms of copper resistance protein CopK Authors: Ash, M.-R. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n7d.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n7d.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/3n7d ftp://data.pdbj.org/pub/pdb/validation_reports/n7/3n7d | HTTPS FTP |
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-Related structure data
Related structure data | 3n7eC 3dsoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8294.567 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: copK / Plasmid: pCX07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AD3 #2: Chemical | #3: Chemical | ChemComp-CU1 / | #4: Water | ChemComp-HOH / | Nonpolymer details | LINK RECORDS BETWEEN CU B 75 AND GLU B 29 HAVE BEEN OMITTED DUE TO AMBIGUITY IN THEIR ROLE IN METAL ...LINK RECORDS BETWEEN CU B 75 AND GLU B 29 HAVE BEEN OMITTED DUE TO AMBIGUITY IN THEIR ROLE IN METAL COORDINATI | |
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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: 1.751525 Å3/Da / Density % sol: 29.775499 % / Mosaicity: 0.619 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M sodium acetate pH 3.8, 0.2M ammonium acetate, 32% (w/v) PEG 4000, 22mM NiCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.3776 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3776 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→50 Å / Num. all: 6136 / Num. obs: 6136 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.114 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.149→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 8.7 / Num. unique all: 622 / Χ2: 1.07 / % possible all: 96.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DSO Resolution: 2.149→24.852 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.34 / Isotropic thermal model: Isotropic with TLS / Cross valid method: Throught / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.142 Å2 / ksol: 0.415 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.54 Å2 / Biso mean: 49.489 Å2 / Biso min: 23.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.149→24.852 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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