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Yorodumi- PDB-4bd0: X-ray structure of a perdeuterated Toho-1 R274N R276N double muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bd0 | |||||||||
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Title | X-ray structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB) | |||||||||
Components | BETA-LACTAMASE TOHO-1 | |||||||||
Keywords | HYDROLASE / PERDEUTERATED NEUTRON STRUCTURE / EXTENDED-SPECTRUM BETA LACTAMASES / CTX- M-TYPE ESBLS | |||||||||
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 BL21 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.207 Å | |||||||||
Authors | Tomanicek, S.J. / Weiss, K.L. / Standaert, R.F. / Ostermann, A. / Schrader, T.E. / Ng, J.D. / Coates, L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Neutron and X-Ray Crystal Structures of a Perdeuterated Enzyme Inhibitor Complex Reveal the Catalytic Proton Network of the Toho-1 Beta-Lactamase for the Acylation Reaction. Authors: Tomanicek, S.J. / Standaert, R.F. / Weiss, K.L. / Ostermann, A. / Schrader, T.E. / Ng, J.D. / Coates, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bd0.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bd0.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 4bd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bd0_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 4bd0_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 4bd0_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4bd0_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/4bd0 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/4bd0 | HTTPS FTP |
-Related structure data
Related structure data | 4bd1C 2zq8S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28104.713 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-291 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI BL21 (bacteria) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: Q47066, beta-lactamase | ||||
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#2: Chemical | ChemComp-BZB / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Nonpolymer details | BENZO[B]THIOPHENE-2-BORONIC ACID (BZB): PERDEUTERA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.35 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 2.0 M AMMONIUM SULFATE AND 0.1 M SODIUM CITRATE PD 5.1 PREPARED IN 99.9 PERCENT D2O AT 20 C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→26.41 Å / Num. obs: 91485 / % possible obs: 99.9 % / Observed criterion σ(I): 2.9 / Redundancy: 10.1 % / Biso Wilson estimate: 8.37 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.21→1.27 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZQ8 Resolution: 1.207→26.408 Å / SU ML: 0.07 / σ(F): 1.35 / Phase error: 9.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.207→26.408 Å
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Refine LS restraints |
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LS refinement shell |
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