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Yorodumi- PDB-4euz: Crystal structure of serratia fonticola carbapenemase SFC-1 S70A-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4euz | ||||||
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Title | Crystal structure of serratia fonticola carbapenemase SFC-1 S70A-Meropenem complex | ||||||
Components | Carbapenem-hydrolizing beta-lactamase SFC-1 | ||||||
Keywords | HYDROLASE/Antibiotic / CARBAPENEMASE / HYDROLASE / ANTIBIOTIC RESISTANCE / BETA-LACTAMASE COMPLEX / HYDROLASE-Antibiotic complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Serratia fonticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Fonseca, F. / Spencer, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: The basis for carbapenem hydrolysis by class A beta-lactamases: a combined investigation using crystallography and simulations. Authors: Fonseca, F. / Chudyk, E.I. / van der Kamp, M.W. / Correia, A. / Mulholland, A.J. / Spencer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4euz.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4euz.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 4euz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4euz_validation.pdf.gz | 712.3 KB | Display | wwPDB validaton report |
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Full document | 4euz_full_validation.pdf.gz | 715.2 KB | Display | |
Data in XML | 4euz_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 4euz_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/4euz ftp://data.pdbj.org/pub/pdb/validation_reports/eu/4euz | HTTPS FTP |
-Related structure data
Related structure data | 4eqiSC 4ev4C 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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Unit cell |
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-Components
#1: Protein | Mass: 30809.768 Da / Num. of mol.: 1 / Fragment: UNP residues 27-309 / Mutation: S70A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia fonticola (bacteria) / Strain: UTAD54 / Gene: BLASFC-1, SFC-1 / Plasmid: pET26-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6JP75, beta-lactamase | ||||||
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#2: Chemical | ChemComp-MEM / ( | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Sequence details | THE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANCIES BETWEEN THE ...THE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na acetate, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9702 Å | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009 | ||||||||||||
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.9702 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.08→48.732 Å / Num. all: 123160 / Num. obs: 123160 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9 | ||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4EQI Resolution: 1.08→22.42 Å / Num. parameters: 25608 / Num. restraintsaints: 33525 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.19%
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Refine analyze | Num. disordered residues: 41 / Occupancy sum hydrogen: 1961.3 / Occupancy sum non hydrogen: 2603.05 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→22.42 Å
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Refine LS restraints |
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