+Open data
-Basic information
Entry | Database: PDB / ID: 4ulv | ||||||
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Title | Cytochrome c prime from Shewanella frigidimarina | ||||||
Components | CYTOCHROME C, CLASS II | ||||||
Keywords | ELECTRON TRANSPORT / GAS SENSOR | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | SHEWANELLA FRIGIDIMARINA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Manole, A.A. / Kekilli, D. / Dobbin, P.S. / Hough, M.A. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2015 Title: Conformational Control of the Binding of Diatomic Gases to Cytochrome C'. Authors: Manole, A. / Kekilli, D. / Svistunenko, D.A. / Wilson, M.T. / Dobbin, P.S. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ulv.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ulv.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ulv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/4ulv ftp://data.pdbj.org/pub/pdb/validation_reports/ul/4ulv | HTTPS FTP |
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-Related structure data
Related structure data | 4cx9C 2yliS 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
#1: Protein | Mass: 13764.347 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA FRIGIDIMARINA (bacteria) / Plasmid: PMMB503EH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07Z15 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 2.2M AM SULFATE, 0.1M HEPES PH7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→44.8 Å / Num. obs: 62629 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.29→1.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YLI Resolution: 1.29→46.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.856 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.853 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→46.3 Å
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Refine LS restraints |
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