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Yorodumi- PDB-2xlh: REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xlh | |||||||||
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Title | REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS | |||||||||
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: 1.14 Å | |||||||||
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. | |||||||||
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 | 2xlh.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xlh.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xlh ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xlh | HTTPS FTP |
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-Related structure data
Related structure data | 2xl6C 2xl8C 2xldC 2xleC 2xlmC 2xloC 2xlvC 2xlwC 2xm0C 2xm4C 1e84S 2xl5 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 on special symmetry positions |
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-Components
#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) / Strain: NCIB 11015 / Plasmid: PTCP-1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BL26 / References: UniProt: P00138 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-SO4 / |
#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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULPHATE, TRIS-BUFFER PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 23, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→47 Å / Num. obs: 55389 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.5 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E84 Resolution: 1.14→46.47 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.91 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / 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: 10.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→46.47 Å
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Refine LS restraints |
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