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Yorodumi- PDB-5agf: Nitrosyl complex of the D121Q variant of cytochrome c prime from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5agf | |||||||||
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Title | Nitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans | |||||||||
Components | CYTOCHROME C PRIME | |||||||||
Keywords | OXIDOREDUCTASE / PROXIMAL NO / CYTOCHROME / GAS SENSING / NITRIC OXIDE | |||||||||
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: 1.09 Å | |||||||||
Authors | Gahfoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Hough, M.A. / Strange, R.W. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2015 Title: Hydrogen Bonding of the Dissociated Histidine Ligand is not Required for Formation of a Proximal No Adduct in Cytochrome C'. Authors: Ghafoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Strange, R.W. / 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 | 5agf.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5agf.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 5agf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5agf_validation.pdf.gz | 814.6 KB | Display | wwPDB validaton report |
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Full document | 5agf_full_validation.pdf.gz | 815.6 KB | Display | |
Data in XML | 5agf_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5agf_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5agf ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5agf | 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: 13644.483 Da / Num. of mol.: 1 / Mutation: YES 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-NO / |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 2.64 Å3/Da / Density % sol: 53.4 % / 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: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→15.5 Å / Num. obs: 62452 / % possible obs: 97 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.09→1.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.09→46.11 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.351 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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: 16.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→46.11 Å
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Refine LS restraints |
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