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Yorodumi- PDB-4cip: Spectroscopically-validated structure of ferrous cytochrome c pri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cip | |||||||||
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Title | Spectroscopically-validated structure of ferrous cytochrome c prime from Alcaligenes xylosoxidans, reduced using ascorbate | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | OXIDOREDUCTASE / 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 / OTHER / Resolution: 1.22 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 | 4cip.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cip.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cip_validation.pdf.gz | 790.7 KB | Display | wwPDB validaton report |
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Full document | 4cip_full_validation.pdf.gz | 792 KB | Display | |
Data in XML | 4cip_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 4cip_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/4cip ftp://data.pdbj.org/pub/pdb/validation_reports/ci/4cip | HTTPS FTP |
-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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-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: Sugar | ChemComp-ASC / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | PROTOPORPH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % / 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 12, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→45.1 Å / Num. obs: 47035 / % possible obs: 97.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.22→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.22→45.09 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.065 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / 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: 14.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→45.09 Å
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Refine LS restraints |
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