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Yorodumi- PDB-5a91: 15K X-ray ligand free: Exploring the Mechanism of beta-Lactam Rin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a91 | |||||||||
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Title | 15K X-ray ligand free: Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography | |||||||||
Components | Beta-lactamase Toho-1 | |||||||||
Keywords | HYDROLASE / BETA LACTAMASE / NEUTRON CRYSTALLOGRAPHY | |||||||||
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 / OTHER / Resolution: 1.2 Å | |||||||||
Authors | Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography. Authors: Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a91.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a91.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 5a91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a91_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 5a91_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 5a91_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5a91_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a91 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a91 | HTTPS FTP |
-Related 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: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q47066, UniProt: E1ANH6*PLUS, beta-lactamase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 300 ul of a 10 mg/ml protein concentration in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1) prepared in D 2 O. |
-Data collection
Diffraction | Mean temperature: 15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.67 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.67 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→38.41 Å / Num. obs: 86849 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / Rpim(I) all: 0.137 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.2→36.199 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 12.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→36.199 Å
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Refine LS restraints |
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LS refinement shell |
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