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Yorodumi- PDB-3ztz: Cytochrome c prime from alcaligenes xylosoxidans: carbon monooxid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ztz | |||||||||
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Title | Cytochrome c prime from alcaligenes xylosoxidans: carbon monooxide bound L16G variant at 1.05 A resolution: unrestraint refinement | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ACHROMOBACTER XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å | |||||||||
Authors | Antonyuk, S.V. / Rustage, N. / Eady, R.R. / Hasnain, S.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ztz.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ztz.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ztz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ztz_validation.pdf.gz | 776.8 KB | Display | wwPDB validaton report |
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Full document | 3ztz_full_validation.pdf.gz | 783 KB | Display | |
Data in XML | 3ztz_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3ztz_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/3ztz ftp://data.pdbj.org/pub/pdb/validation_reports/zt/3ztz | HTTPS FTP |
-Related structure data
Related structure data | 2ykzC 2yl0C 2yl1C 2yl3C 2yl7C 2yldC 2ylgSC 2yliC 3zqvC 3zqyC 3ztmC 3zwiC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-CMO / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULPHATE, HEPES PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 4, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 74665 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.04→1.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2YLG Resolution: 1.05→10 Å / Num. parameters: 13792 / Num. restraintsaints: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: AT THE LAST RUN OF REFINEMENT R-FREE FLAGS WERE REMOVED AND DATA WERE REFINED AGAINST ALL DATA.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||||||
Refine analyze | Num. disordered residues: 80 / Occupancy sum hydrogen: 877.54 / Occupancy sum non hydrogen: 1219.9 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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