+Open data
-Basic information
Entry | Database: PDB / ID: 1a8t | ||||||
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Title | METALLO-BETA-LACTAMASE IN COMPLEX WITH L-159,061 | ||||||
Components | METALLO-BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / METALLO-BETA-LACTAMASE / ZINC / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Fitzgerald, P.M.D. / Toney, J.H. / Grover, N. / Vanderwall, D. | ||||||
Citation | Journal: Chem.Biol. / Year: 1998 Title: Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-beta-lactamase. Authors: Toney, J.H. / Fitzgerald, P.M. / Grover-Sharma, N. / Olson, S.H. / May, W.J. / Sundelof, J.G. / Vanderwall, D.E. / Cleary, K.A. / Grant, S.K. / Wu, J.K. / Kozarich, J.W. / Pompliano, D.L. / Hammond, G.G. #1: Journal: Biochemistry / Year: 1998 Title: Unanticipated Inhibition of the Metallo-Beta-Lactamase from Bacteroides Fragilis by 4-Morpholineethanesulfonic Acid (Mes): A Crystallographic Study at 1.85-A Resolution Authors: Fitzgerald, P.M. / Wu, J.K. / Toney, J.H. #2: Journal: Protein Expr.Purif. / Year: 1997 Title: High-Yield Expression, Purification, and Characterization of Active, Soluble Bacteroides Fragilis Metallo-Beta-Lactamase, Ccra Authors: Toney, J.H. / Wu, J.K. / Overbye, K.M. / Thompson, C.M. / Pompliano, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a8t.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a8t.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a8t_validation.pdf.gz | 712.4 KB | Display | wwPDB validaton report |
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Full document | 1a8t_full_validation.pdf.gz | 768.4 KB | Display | |
Data in XML | 1a8t_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1a8t_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a8t ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a8t | HTTPS FTP |
-Related structure data
Related structure data | 1a7tS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25387.666 Da / Num. of mol.: 2 / Mutation: A171T, D208N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: TAL3636 / Gene: CCRA / Variant: CLINICAL ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P25910, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-061 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: PROTEIN WAS CRYSTALLIZED FROM 28% PEG 4000, 100 MM SODIUM CHLORIDE, 100 MM SODIUM CACODYLATE BUFFER, PH 6.6 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 18, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→100 Å / Num. obs: 12599 / % possible obs: 75 % / Observed criterion σ(I): 1 / Redundancy: 1.93 % / Biso Wilson estimate: 19.89 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.55→2.71 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.125 / % possible all: 53.8 |
Reflection shell | *PLUS % possible obs: 53.8 % / Num. unique obs: 1468 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A7T Resolution: 2.55→10 Å / Cross valid method: EX POST FACTO / σ(F): 1 Details: THE VALUE OF R-FREE WAS NOT MONITORED DURING THE COURSE OF REFINEMENT.
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Displacement parameters | Biso mean: 8.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.55 Å / Lowest resolution: 2.66 Å / Num. reflection obs: 952 / Rfactor obs: 0.188 |