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Yorodumi- PDB-1o8u: The 2 Angstrom Structure of 6-Oxo Camphor Hydrolase: New Structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o8u | ||||||
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Title | The 2 Angstrom Structure of 6-Oxo Camphor Hydrolase: New Structural Diversity in the Crotonase Superfamily | ||||||
Components | 6-OXO CAMPHOR HYDROLASE | ||||||
Keywords | HYDROLASE / CROTONASE / TERPENE METABOLISM / RHODOCOCCUSE | ||||||
Function / homology | Function and homology information 6-oxocamphor hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances Similarity search - Function | ||||||
Biological species | RHODOCOCCUS ERYTHROPOLIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Grogan, G. / Whittingham, J.L. / Turkenburg, J.P. / Verma, C.S. / Walsh, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The 2 a Crystal Structure of 6-Oxo Camphor Hydrolase: New Structural Diversity in the Crotonase Superfamily Authors: Whittingham, J.L. / Turkenburg, J.P. / Verma, C.S. / Walsh, M.A. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o8u.cif.gz | 302.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o8u.ent.gz | 255.1 KB | Display | PDB format |
PDBx/mmJSON format | 1o8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8u ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE SIX MOLECULES IN THE ASYMMETRIC UNIT FORM ONECOMPLETE HEXAMER. |
-Components
#1: Protein | Mass: 28513.238 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Strain: NCIMB 9784 / Plasmid: PET26B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q93TU6 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SWISS-PROT DATABASE REFERENCE IS FROM THE GENERIC PARENT OF THE SPECIES (STRAIN NCIMB 9784) ...THE SWISS-PROT DATABASE REFERENCE IS FROM THE GENERIC PARENT OF THE SPECIES (STRAIN NCIMB 9784) DESCRIBED IN THIS EXPERIMENT | |
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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: 2.2 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: VAPOUR DIFFUSION HANGING DROP PROTEIN SOLUTION: 10 MG/ML IN 50 MM TRIS-HCL PH 7.0, 1 MM DTT, 20 MICROMOLAR PMSF RESERVOIR: 0.1 M SODIUM ACETATE,0.2 M AMMONIUM SULPHATE, 28% (V/V) PEG 4K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97900,0.97937,0.88560 | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2001 / Details: MIRRORS | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. obs: 95532 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.8 | ||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7.1 / % possible all: 97 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 2.4 % | ||||||||||||
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.249 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN EACH OF THE SIX MOLECULES OF THE ASYMMETRIC UNIT, THE FIRST 2-4 RESIDUES ARE DISORDERED AND THE LAST 4 RESIDUES ARE DISORDERED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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