+Open data
-Basic information
Entry | Database: PDB / ID: 3g4p | ||||||
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Title | OXA-24 beta-lactamase at pH 7.5 | ||||||
Components | Beta-lactamase OXA-24 | ||||||
Keywords | HYDROLASE / B-LACTAMASES / ENZYME MECHANISM / CARBAPENEM / RESISTANCE | ||||||
Function / homology | Function and homology information penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Santillana, E. / Romero, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase Authors: Bou, G. / Santillana, E. / Sheri, A. / Beceiro, A. / Sampson, J.M. / Kalp, M. / Bethel, C.R. / Distler, A.M. / Drawz, S.M. / Pagadala, S.R. / van den Akker, F. / Bonomo, R.A. / Romero, A. / Buynak, J.D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis Authors: Santillana, E. / Beceiro, A. / Bou, G. / Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g4p.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g4p.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g4p ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g4p | HTTPS FTP |
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-Related structure data
Related structure data | 3fv7C 3fyzC 3fzcC 3mbzC 2jc7S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27586.660 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: oxa-24 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8RLA6, beta-lactamase |
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#2: 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: 3.98 Å3/Da / Density % sol: 69.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M SODIUM ACETATE, 28% PEG 2000 MME, 0.1M HEPES (PH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2008 |
Radiation | Monochromator: SINGLE SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→31.59 Å / Num. all: 32135 / Num. obs: 32064 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 24.04 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4548 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2jc7 Resolution: 1.97→30.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.702 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.129 / 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: 30 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→30.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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