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- PDB-2yli: RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yli | |||||||||
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Title | RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS IN ITS FERROUS FORM AT 1.45 A | |||||||||
![]() | CYTOCHROME C' | |||||||||
![]() | ELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE | |||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S. | |||||||||
![]() | ![]() Title: Carbon Monoxide Poisoning is Prevented by the Energy Costs of Conformational Changes in Gas- Binding Haemproteins. Authors: Antonyuk, S.V. / Rustage, N. / Petersen, C.A. / Arnst, J.L. / Heyes, D.J. / Sharma, R. / Berry, N.G. / Scrutton, N.S. / Eady, R.R. / Andrew, C.R. / Hasnain, S.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.9 KB | Display | ![]() |
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Full document | ![]() | 794.2 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ykzSC ![]() 2yl0C ![]() 2yl1C ![]() 2yl3C ![]() 2yl7C ![]() 2yldC ![]() 2ylgC ![]() 3zqvC ![]() 3zqyC ![]() 3ztmC ![]() 3ztzC ![]() 3zwiC C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 13631.442 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULPHATE, TRIS PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR / Detector: CCD / Date: Mar 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→23 Å / Num. obs: 27081 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YKZ Resolution: 1.45→46.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.233 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.064 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.135 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→46.13 Å
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Refine LS restraints |
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