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Yorodumi- PDB-2xf3: Structural and mechanistic studies on a cephalosporin esterase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xf3 | ||||||
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Title | Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway | ||||||
Components | ORF12 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Iqbal, A. / Valegard, K. / Kershaw, N.J. / Ivison, D. / Genereux, C. / Dubus, A. / Andersson, I. / Schofield, C.J. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013 Title: Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway. Authors: Valegard, K. / Iqbal, A. / Kershaw, N.J. / Ivison, D. / Genereux, C. / Dubus, A. / Blikstad, C. / Demetriades, M. / Hopkinson, R.J. / Lloyd, A.J. / Roper, D.I. / Schofield, C.J. / Andersson, I. / McDonough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xf3.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xf3.ent.gz | 157.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/2xf3 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xf3 | HTTPS FTP |
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-Related structure data
Related structure data | 2xepSC 2xfsC 2xftC 2xgnC 2xh9C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49901.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 2 MOLECULES OF CLAVULANIC ACID ARE BOUND PER SUBUNIT Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83Z62, UniProt: Q8KRB7*PLUS #2: Chemical | ChemComp-J01 / ( #3: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 8 Details: 13%(W/V) PEG 4000, 0.1M NAAC, 0.1M NACL, 10% GLYCEROL, 0.1M TRIS/HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755 |
Detector | Date: Jul 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35 Å / Num. obs: 139836 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.25 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XEP Resolution: 1.55→81.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.221 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.077 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→81.65 Å
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Refine LS restraints |
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