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Yorodumi- PDB-2xle: Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xle | |||||||||
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Title | Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K variant with bound NO | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ACHROMOBACTER XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 | 2xle.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xle.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xle ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xle | HTTPS FTP |
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-Related structure data
Related structure data | 2xl6C 2xl8C 2xldC 2xlhC 2xlmC 2xloC 2xlvC 2xlwC 2xm0C 2xm4C 2xl5 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
#1: Protein | Mass: 13603.429 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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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-NO / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULPHATE, HEPES PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2007 / 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: 1.12→37 Å / Num. obs: 57744 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 15.53 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.1 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.12→37 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.133 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / 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: 10.729 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→37 Å
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Refine LS restraints |
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