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- PDB-2xf3: Structural and mechanistic studies on a cephalosporin esterase fr... -
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Open data
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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 | ||||||
![]() | ORF12 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iqbal, A. / Valegard, K. / Kershaw, N.J. / Ivison, D. / Genereux, C. / Dubus, A. / Andersson, I. / Schofield, C.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.4 KB | Display | ![]() |
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PDB format | ![]() | 157.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 66.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xepSC ![]() 2xfsC ![]() 2xftC ![]() 2xgnC ![]() 2xh9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-J01 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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