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- PDB-5js5: Nitric oxide complex of the L16F mutant of cytochrome c prime fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5js5 | |||||||||
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Title | Nitric oxide complex of the L16F 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 | ![]() | 69.2 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.9 KB | Display | ![]() |
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Full document | ![]() | 813.8 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jliC ![]() 5jp7C ![]() 5jraC ![]() 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
#1: Protein | Mass: 13407.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pet26b+ / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEC / |
#3: Sugar | ChemComp-ASC / |
#4: Chemical | ChemComp-NO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2M Ammonium sulfate 0.1M 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 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: 1.7→46.08 Å / Num. obs: 17754 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 12.7 / Num. measured all: 109533 / Scaling rejects: 105 | |||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2YLI Resolution: 1.7→46.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.1113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.116 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 107.91 Å2 / Biso mean: 34.44 Å2 / Biso min: 21.97 Å2
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Refinement step | Cycle: final / Resolution: 1.7→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.958 Å / Origin y: 41.645 Å / Origin z: 19.993 Å
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