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Yorodumi- PDB-2jc7: The crystal structure of the carbapenemase OXA-24 reveals new ins... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jc7 | ||||||
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Title | The crystal structure of the carbapenemase OXA-24 reveals new insights into the mechanism of carbapenem-hydrolysis | ||||||
Components | BETA-LACTAMASE OXA-24 | ||||||
Keywords | HYDROLASE / PLASMID / B-LACTAMASES / ENZYME MECHANISM / CARBAPENEM RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ACINETOBACTER BAUMANNII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Santillana, E. / Romero, A. | ||||||
Citation | 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 | 2jc7.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jc7.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jc7 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jc7 | HTTPS FTP |
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-Related structure data
Related structure data | 1k57S 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
#1: Protein | Mass: 27543.658 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RLA6, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 1 TO 21 COMPRISED THE SIGNAL PEPTIDE AND ARE NOT PRESENT IN THE RECOMBINANT PROTEIN ...RESIDUES 1 TO 21 COMPRISED THE SIGNAL PEPTIDE AND ARE NOT PRESENT IN THE RECOMBINAN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 68.75 % |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 6.5, 2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→55 Å / Num. obs: 16630 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.48→2.62 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K57 Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1439570.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.4546 Å2 / ksol: 0.384349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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