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Yorodumi- PDB-4cdv: Spectroscopically-validated structure of cytochrome c prime from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cdv | |||||||||
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Title | Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 100K | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / RESONANCE RAMAN / VALIDATION / GAS SENSOR / LIGAND DISCRIMINATION / FERRIC / HAEM / HEME / RADIOLYSIS | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ACHROMOBACTER XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | |||||||||
Authors | Kekilli, D. / Dworkowski, F. / Antonyuk, S. / Hough, M.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Fingerprinting Redox and Ligand States in Haemprotein Crystal Structures Using Resonance Raman Spectroscopy. Authors: Kekilli, D. / Dworkowski, F.S. / Pompidor, G. / Fuchs, M.R. / Andrew, C.R. / Antonyuk, S. / Strange, R.W. / Eady, R.R. / Hasnain, S.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 | 4cdv.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cdv.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cdv_validation.pdf.gz | 783.6 KB | Display | wwPDB validaton report |
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Full document | 4cdv_full_validation.pdf.gz | 783.5 KB | Display | |
Data in XML | 4cdv_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4cdv_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/4cdv ftp://data.pdbj.org/pub/pdb/validation_reports/cd/4cdv | HTTPS FTP |
-Related structure data
Related structure data | 4cdaC 4cdyC 4cipC 4cjgC 4cjoC 2yliS C: citing same article (ref.) S: Starting model for refinement |
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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: 13631.442 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULFATE, HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→46.1 Å / Num. obs: 49558 / % possible obs: 95 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.17→1.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.6 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YLI Resolution: 1.17→46.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.849 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / 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: 9.939 Å2
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Refinement step | Cycle: LAST / Resolution: 1.17→46.14 Å
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Refine LS restraints |
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