+Open data
-Basic information
Entry | Database: PDB / ID: 6hb8 | ||||||
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Title | Crystal structure of OXA-517 beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Raczynska, J.E. / Dabos, L. / Zavala, A. / Retailleau, P. / Iorga, B. / Jaskolski, M. / Naas, T. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Genetic, biochemical and structural characterization of OXA-517, an OXA-48-like extended-spectrum cephalosporins and carbapenems-hydrolyzing beta-lactamase Authors: Dabos, L. / Raczynska, J.E. / Bogaerts, P. / Zavala, A. / Bonnin, R.A. / Peyrat, A. / Retailleau, P. / Iorga, B. / Jaskolski, M. / Glupczynski, Y. / Naas, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hb8.cif.gz | 232.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hb8.ent.gz | 186.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hb8 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hb8 | HTTPS FTP |
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-Related structure data
Related structure data | 4s2pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29639.518 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Plasmid: pET41b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U8YI81, beta-lactamase |
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-Non-polymers , 6 types, 761 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ETX / | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: 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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5 and 20% (w/v) PEG10000 / PH range: 293 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980104506016 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980104506016 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→46.18 Å / Num. obs: 84548 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.16 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.86→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 13554 / CC1/2: 0.35 / Rrim(I) all: 1.25 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4s2p Resolution: 1.86→46.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.644 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.138 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.753 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→46.18 Å
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Refine LS restraints |
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