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Yorodumi- PDB-2xl6: Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124A v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xl6 | |||||||||
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Title | Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124A variant with bound NO | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | |||||||||
Authors | Hough, M.A. / Antonyuk, S.V. / Hasnain, S.S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Distal-to-Proximal No Conversion in Hemoproteins: The Role of the Proximal Pocket. Authors: Hough, M.A. / Antonyuk, S.V. / Barbieri, S. / Rustage, N. / Mckay, A.L. / Servid, A.E. / 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 | 2xl6.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xl6.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 2xl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xl6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2xl6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2xl6_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2xl6_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xl6 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xl6 | HTTPS FTP |
-Related structure data
Related structure data | 2xl8C 2xldC 2xleC 2xlhSC 2xlmC 2xloC 2xlvC 2xlwC 2xm0C 2xm4C 2xl5 S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13545.326 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) / References: UniProt: P00138 |
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-Non-polymers , 5 types, 362 molecules
#2: Chemical | ChemComp-HEC / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NO / | #5: Chemical | ChemComp-NO3 / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEEREDSequence details | MUTATION R124A | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.97 % / Description: NONE |
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Crystal grow | Details: AMMONIUM SULPHATE, TRIS PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.725 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.725 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→40 Å / Num. obs: 67775 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.07→1.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.8 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XLH Resolution: 1.07→45.83 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.728 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / 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: 8.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→45.83 Å
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Refine LS restraints |
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