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Yorodumi- PDB-4wwd: High-resolution structure of the Co-bound form of the Y135F mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wwd | ||||||
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Title | High-resolution structure of the Co-bound form of the Y135F mutant of C. metallidurans CnrXs | ||||||
Components | Nickel and cobalt resistance protein CnrR | ||||||
Keywords | METAL BINDING PROTEIN / Nickel sensor | ||||||
Function / homology | Heavy-metal resistance protein / Heavy-metal resistance / periplasmic space / : / CARBON DIOXIDE / FORMIC ACID / : / Nickel and cobalt resistance protein CnrR Function and homology information | ||||||
Biological species | Ralstonia metallidurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Volbeda, A. / Coves, J. / Maillard, A.P. / Kuennemann, S. / Grosse, C. / Schleuder, G. / Petit-Haertlein, I. / de Rosny, E. / Nies, D.H. | ||||||
Citation | Journal: Metallomics / Year: 2015 Title: Response of CnrX from Cupriavidus metallidurans CH34 to nickel binding. Authors: Maillard, A.P. / Kunnemann, S. / Groe, C. / Volbeda, A. / Schleuder, G. / Petit-Hartlein, I. / de Rosny, E. / Nies, D.H. / Coves, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wwd.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wwd.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/4wwd ftp://data.pdbj.org/pub/pdb/validation_reports/ww/4wwd | HTTPS FTP |
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-Related 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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Details | biological unit is the same as asym. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13295.874 Da / Num. of mol.: 1 / Fragment: Metal-sensor domain of CnrX, UNP residues 31-148 / Mutation: Y135F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: cnrR, cnrX, Rmet_6206, RMe0087 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37975 |
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-Non-polymers , 6 types, 240 molecules
#2: Chemical | ChemComp-CO / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-CO2 / | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-FMT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, NaH2P04/KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979725 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979725 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.11→20 Å / Num. obs: 78323 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 11.253 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.11 / Χ2: 1.035 / Net I/σ(I): 12.29 / Num. measured all: 618117 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→19.79 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.134 / FOM work R set: 0.9244 / SU B: 1.638 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0514 / SU Rfree: 0.0505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.13 Å2 / Biso mean: 12.327 Å2 / Biso min: 3.59 Å2
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Refinement step | Cycle: final / Resolution: 1.3→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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