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Yorodumi- PDB-2a3u: Crystal structure of sulbactam bound to E166A variant of SHV-1 be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a3u | ||||||
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Title | Crystal structure of sulbactam bound to E166A variant of SHV-1 beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / INHIBITOR DESIGN / COVALENT INTERMEDIATE | ||||||
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 pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Carey, P.R. / Bonomo, R.A. / van den Akker, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: High Resolution Crystal Structures of the trans-Enamine Intermediates Formed by Sulbactam and Clavulanic Acid and E166A SHV-1 {beta}-Lactamase. Authors: Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Carey, P.R. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
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Remark 600 | HETEROGEN ONLY PART OF THE MOLECULE EPE IS VISIBLE AND MODELED. THE MOLECULE MA4 HAS ONE MOLECULE ...HETEROGEN ONLY PART OF THE MOLECULE EPE IS VISIBLE AND MODELED. THE MOLECULE MA4 HAS ONE MOLECULE THAT IS PRESENT IN ITS ENTIRITY, THE SECOND HAS A SMALLER PART THAT IS VISIBLE.THE COMPOUND TSL IS COVALENTLY REACTED WITH THE ACTIVE SITE SER70 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a3u.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a3u.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 2a3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/2a3u ftp://data.pdbj.org/pub/pdb/validation_reports/a3/2a3u | 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
#1: Protein | Mass: 29419.725 Da / Num. of mol.: 1 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Production host: Escherichia coli (E. coli) References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase | ||||
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#2: Chemical | ChemComp-TSL / | ||||
#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.87 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Sep 4, 2004 |
Radiation | Monochromator: FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→30 Å / Num. all: 52442 / Num. obs: 52285 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→27.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1265615.9 / Data cutoff high rms absF: 1265615.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 81.0505 Å2 / ksol: 0.459515 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.34→27.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.42 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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