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Yorodumi- PDB-2zqa: Cefotaxime acyl-intermediate structure of class a beta-lacta Toho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zqa | |||||||||
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Title | Cefotaxime acyl-intermediate structure of class a beta-lacta Toho-1 E166A/R274N/R276N triple mutant | |||||||||
Components | Beta-lactamase Toho-1 | |||||||||
Keywords | HYDROLASE / EXTENDED-SPECTRUM / ESBL / BETA-LACTAMASE / ACYL-ENZYME / COMPLEX / CEFOTAXIME / TOHO-1 / 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | |||||||||
Authors | Nitanai, Y. / Shimamura, T. / Uchiyama, T. / Ishii, Y. / Takehira, M. / Yutani, K. / Matsuzawa, H. / Miyano, M. | |||||||||
Citation | Journal: To be Published Title: Structural Basis of Extend Spectrum Beta-Lactamase in Correlation of Enzymatic Kinetics and Thermal Stability of Acyl-Intermediates Authors: Nitanai, Y. / Shimamura, T. / Uchiyama, T. / Ishii, Y. / Takehira, M. / Yutan, K. / Matsuzawa, H. / Miyano, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zqa.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zqa.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zqa ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zqa | HTTPS FTP |
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-Related structure data
Related structure data | 2zq9C 2zqcC 2zqdC 2zq7S 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: 28117.752 Da / Num. of mol.: 1 / Mutation: E166A, R274N, R276N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: PUC119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47066, beta-lactamase | ||
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#2: Chemical | ChemComp-CEF / | ||
#3: Chemical | ChemComp-SO4 / #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: 2.63 Å3/Da / Density % sol: 53.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 / Wavelength: 0.8 Å | |||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 11, 2007 / Details: mirrors | |||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 0.95→50 Å / Num. obs: 186625 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 25.88 | |||||||||
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.77 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZQ7 Resolution: 0.95→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.331 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / 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: 10.501 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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