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Yorodumi- PDB-5jra: Nitric oxide complex of the L16V mutant of cytochrome c prime fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jra | |||||||||
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Title | Nitric oxide complex of the L16V mutant of cytochrome c prime from Alcaligenes xylosoxidans | |||||||||
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: 1.38 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 | 5jra.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jra.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jra_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5jra_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5jra_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5jra_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jra ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jra | HTTPS FTP |
-Related structure data
Related structure data | 5jliC 5jp7C 5js5C 5jslC 5jt4C 5juaC 5jveC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 13488.234 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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#3: Sugar | ChemComp-ASC / |
-Non-polymers , 4 types, 141 molecules
#2: Chemical | ChemComp-HEC / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-NO / |
#6: 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: 2.74 Å3/Da / Density % sol: 55.04 % |
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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: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→46.072 Å / Num. obs: 32339 / % possible obs: 100 % / Redundancy: 7.6 % / Rsym value: 0.051 / Net I/av σ(I): 6.87 / Net I/σ(I): 15.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLI Resolution: 1.38→46.07 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.409 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.34 Å2 / Biso mean: 24.331 Å2 / Biso min: 12.75 Å2
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Refinement step | Cycle: final / Resolution: 1.38→46.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.416 Å / Total num. of bins used: 20
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