+Open data
-Basic information
Entry | Database: PDB / ID: 3e6b | ||||||
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Title | OCPA complexed CprK (C200S) | ||||||
Components | Cyclic nucleotide-binding protein | ||||||
Keywords | TRANSCRIPTION REGULATION / CprK / Halorespiration / transcriptional regulator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Levy, C. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2008 Title: Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator Authors: Levy, C. / Pike, K. / Heyes, D.J. / Joyce, M.G. / Gabor, K. / Smidt, H. / van der Oost, J. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e6b.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6b.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 3e6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6b_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 3e6b_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 3e6b_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3e6b_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6b ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6b | HTTPS FTP |
-Related structure data
Related structure data | 3e5qC 3e5uC 3e5xC 3e6cC 3e6dC 3e6x 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
#1: Protein | Mass: 28379.617 Da / Num. of mol.: 2 / Mutation: C200S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Strain: DCB-2 / Gene: Dhaf_0678 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18R04, UniProt: B8FW11*PLUS #2: Chemical | #3: 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: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 294 K / pH: 6 Details: 100mM MES, 10% MPD, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.012→40.26 Å / Num. obs: 29505 |
-Processing
Software | Name: REFMAC / Version: 5.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→40.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.516 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→40.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.06 Å / Total num. of bins used: 20
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