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Yorodumi- PDB-3byd: Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca -
+Open data
-Basic information
Entry | Database: PDB / ID: 3byd | ||||||
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Title | Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca | ||||||
Components | Beta-lactamase OXY-1 | ||||||
Keywords | HYDROLASE / Multi-domain proteins (alpha and beta) / Antibiotic resistance | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella oxytoca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å | ||||||
Authors | Liang, Y.-H. / Wu, S.W. / Su, X.-D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural insights into the broadened substrate profile of the extended-spectrum beta-lactamase OXY-1-1 from Klebsiella oxytoca Authors: Liang, Y.-H. / Gao, R. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3byd.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3byd.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3byd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3byd_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 3byd_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 3byd_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3byd_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/3byd ftp://data.pdbj.org/pub/pdb/validation_reports/by/3byd | HTTPS FTP |
-Related structure data
Related structure data | 1bzaS 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: 28606.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pQESW-9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P22391, beta-lactamase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: 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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25%(w/v) PEG 4000, 0.1M sodium acetate buffer, 0.2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0292 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→56 Å / Num. obs: 21787 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.071 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.129 / Num. unique all: 2091 / Χ2: 0.758 / % possible all: 96.1 |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BZA Resolution: 1.93→55.47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.489 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.218 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→55.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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