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Yorodumi- PDB-5jve: L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jve | |||||||||
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Title | L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state | |||||||||
Components | Cytochrome c' | |||||||||
Keywords | ELECTRON TRANSPORT / gas sensor / cytochrome / 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 | Alcaligenes xylosoxydans xylosoxydans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | |||||||||
Authors | Kekilli, D. / Strange, R.W. / Hough, M.A. | |||||||||
Citation | Journal: Chem Sci / Year: 2017 Title: Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design. Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N. ...Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N.S. / Andrew, C.R. / 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 | 5jve.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jve.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jve_validation.pdf.gz | 784 KB | Display | wwPDB validaton report |
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Full document | 5jve_full_validation.pdf.gz | 784.5 KB | Display | |
Data in XML | 5jve_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5jve_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jve ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jve | HTTPS FTP |
-Related structure data
Related structure data | 5jliC 5jp7C 5jraC 5js5C 5jslC 5jt4C 5juaC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13373.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria) Plasmid: pet26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00138 |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 55.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2M Ammonium sulfate, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2015 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→44.8 Å / Num. obs: 61939 / % possible obs: 98.7 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLI Resolution: 1.12→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Displacement parameters | Biso max: 68.89 Å2 / Biso mean: 18.1983 Å2 / Biso min: 8.7 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.12→10 Å
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Refine LS restraints |
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