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- PDB-2yld: RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yld | |||||||||
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Title | RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A | |||||||||
![]() | CYTOCHROME C' | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Antonyuk, S.V. / Rustage, N. / 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 | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 93.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ykzSC ![]() 2yl0C ![]() 2yl1C ![]() 2yl3C ![]() 2yl7C ![]() 2ylgC ![]() 2yliC ![]() 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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/ASC.gif)
![](data/chem/img/ASC.gif)
#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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#4: Sugar | ChemComp-ASC / ![]() |
-Non-polymers , 4 types, 257 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEC / ![]() | ||
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#3: Chemical | ChemComp-CMO / ![]() | ||
#5: Chemical | ![]() #6: 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: MARRESEARCH / Detector: CCD / Date: Sep 12, 2008 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→36 Å / Num. obs: 40961 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 81.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2YKZ Resolution: 1.25→46.68 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.563 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / 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: 19.463 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→46.68 Å
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Refine LS restraints |
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