+Open data
-Basic information
Entry | Database: PDB / ID: 3bfg | ||||||
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Title | class A beta-lactamase SED-G238C complexed with meropenem | ||||||
Components | Class A beta-lactamase Sed1 | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS A / SED-G238C / MEROPENEM / ACYL-ENZYME | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Citrobacter sedlakii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pernot, L. / Petrella, S. / Sougakoff, W. | ||||||
Citation | Journal: To be Published Title: acyl-intermediate structures of the class A beta-lactamase SED-G238C Authors: Pernot, L. / Petrella, S. / Sougakoff, W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii Authors: Petrella, S. / Pernot, L. / Sougakoff, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bfg.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfg.ent.gz | 180.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfg ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfg | HTTPS FTP |
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-Related structure data
Related structure data | 3bfdSC 3bfeC 3bffC S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 28330.221 Da / Num. of mol.: 4 / Fragment: SED-G238C, UNP residues 34-295 / Mutation: G238C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter sedlakii (bacteria) / Strain: 2596 / Gene: bla-SED-1 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93PQ0, beta-lactamase #2: Chemical | ChemComp-MER / ( #3: Water | ChemComp-HOH / | Sequence details | THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. THREE NUMBERS, 58, 239, AND 253 WERE ...THIS COORDINATE | |
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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: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35% PEG MME 2000, 200mM KSCN, 100mM SODIUM CACODYLATE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 16, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.1 Å / Num. all: 75348 / Num. obs: 75348 / % possible obs: 92.2 % / Redundancy: 3.5 % / Rsym value: 0.104 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 8338 / Rsym value: 0.317 / % possible all: 70.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BFD Resolution: 2→34.1 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016
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