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Yorodumi- PDB-3bfe: Crystal Structure of the Class A beta-lactamase SED-1 from Citrob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bfe | ||||||
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Title | Crystal Structure of the Class A beta-lactamase SED-1 from Citrobacter sedlakii | ||||||
Components | Class A beta-lactamase Sed1 | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS A / SED-1 | ||||||
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: 2.4 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 | 3bfe.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfe.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bfe_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 3bfe_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 3bfe_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 3bfe_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfe ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfe | HTTPS FTP |
-Related structure data
Related structure data | 3bfdSC 3bffC 3bfgC 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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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: 28284.127 Da / Num. of mol.: 4 / Fragment: SED-1, UNP residues 34-295 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-SCN / | #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: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 35% PEG 10000, 200mM KSCN, 100mM Tris-HCL pH8.5, 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: 2.4→29.31 Å / Num. all: 42772 / Num. obs: 42772 / % possible obs: 89.4 % / Redundancy: 2.5 % / Rsym value: 0.107 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 5688 / Rsym value: 0.165 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BFD Resolution: 2.4→29.31 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017
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