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- PDB-5jra: Nitric oxide complex of the L16V mutant of cytochrome c prime fro... -
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Open data
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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 | |||||||||
![]() | Cytochrome c' | |||||||||
![]() | ELECTRON TRANSPORT / gas sensor cytochrome nitric oxide | |||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kekilli, D. / Strange, R.W. / Hough, M.A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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![](data/chem/img/ASC.gif)
![](data/chem/img/ASC.gif)
#1: Protein | Mass: 13488.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pet26b+ / Production host: ![]() ![]() |
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#3: Sugar | ChemComp-ASC / |
-Non-polymers , 4 types, 141 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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