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Yorodumi- PDB-5g18: Direct Observation of Active-site Protonation States in a Class A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g18 | |||||||||
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Title | Direct Observation of Active-site Protonation States in a Class A beta lactamase with a monobactam substrate | |||||||||
Components | BETA-LACTAMASE CTX-M-97 | |||||||||
Keywords | HYDROLASE / BETA LACTAMASE / TOHO / NEUTRON | |||||||||
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: 1.1 Å | |||||||||
Authors | Vandavasi, V.G. / Weiss, K.L. / Parks, J.M. / Cooper, J.B. / Ginell, S.L. / Coates, L. | |||||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2017 Title: Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A beta-Lactamase with a Monobactam Substrate. Authors: Vandavasi, V.G. / Langan, P.S. / Weiss, K.L. / Parks, J.M. / Cooper, J.B. / 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 | 5g18.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g18.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g18 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g18 | HTTPS FTP |
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-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 / Fragment: RESIDUES 30-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: E1ANH6, UniProt: Q47066*PLUS, beta-lactamase | ||||
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#2: Chemical | ChemComp-AZR / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Nonpolymer details | AZTREONAM (AZR): BOUND TO SER 70 | |
-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: 53.23 % / Description: NONE |
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Crystal grow | pH: 6.1 / Details: pH 6.1 |
-Data collection
Diffraction | Mean temperature: 15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→32.5 Å / Num. obs: 113081 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 6.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.1→32.537 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 10.91 / 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: 1.1→32.537 Å
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Refine LS restraints |
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LS refinement shell |
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