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Yorodumi- PDB-3bfd: Crystal Structure of the Class A beta-lactamase SED-G238C mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bfd | ||||||
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Title | Crystal Structure of the Class A beta-lactamase SED-G238C mutant from Citrobacter sedlakii | ||||||
Components | Class A beta-lactamase Sed1 | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS A / SED-G238C MUTANT | ||||||
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 | 3bfd.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfd.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bfd_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 3bfd_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 3bfd_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 3bfd_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfd ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfd | HTTPS FTP |
-Related structure data
Related structure data | 3bfeC 3bffC 3bfgC 1bzaS C: citing same article (ref.) 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 28445.307 Da / Num. of mol.: 4 / Fragment: SED-G238C, UNP residues 33-295 / 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-CAC / #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: 2.66 Å3/Da / Density % sol: 53.8 % |
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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: 0.97887 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 18, 2002 |
Radiation | Monochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97887 Å / Relative weight: 1 |
Reflection | Resolution: 2→16.7 Å / Num. all: 80352 / Num. obs: 80352 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rsym value: 0.102 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 11334 / Rsym value: 0.33 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BZA Resolution: 2→16.7 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.92 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→16.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008
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