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Yorodumi- PDB-1rgy: Citrobacter freundii GN346 Class C beta-Lactamase Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rgy | ||||||
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Title | Citrobacter freundii GN346 Class C beta-Lactamase Complexed with Transition-State Analog of Cefotaxime | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / cephalosporinase / enzyme inhibition / phosphonate / beta-lactam antibiotics / drug design | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Citrobacter freundii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Nukaga, M. / Kumar, S. / Nukaga, K. / Pratt, R.F. / Knox, J.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes. Authors: Nukaga, M. / Kumar, S. / Nukaga, K. / Pratt, R.F. / Knox, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rgy.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rgy.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/1rgy ftp://data.pdbj.org/pub/pdb/validation_reports/rg/1rgy | HTTPS FTP |
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-Related structure data
Related structure data | 1rgzC 1fr1S 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: 39834.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: BLA / Plasmid details: pHSG398 derivative / Plasmid: pCFC-plac-1 / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: P05193, beta-lactamase |
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#2: Chemical | ChemComp-PTX / {[( |
#3: Chemical | ChemComp-MPD / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 8000, HEPES, MPD, Urea, phosphonate inhibitor, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. all: 56830 / Num. obs: 56830 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.095 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5391 / Rsym value: 0.904 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FR1 Resolution: 1.52→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1336854.26 / Data cutoff high rms absF: 1336854.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.8805 Å2 / ksol: 0.316854 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.52→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.62 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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