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Yorodumi- PDB-2h0t: Crystal structure of the M69V E166A double mutant of SHV-1 b-lact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h0t | ||||||
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Title | Crystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to clavulanic acid | ||||||
Components | Broad-spectrum beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / Antibiotic resistance / b-lactamase inhibitor | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | van den Akker, F. / Padayatti, P.S. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine beta-lactamase intermediates. Authors: Totir, M.A. / Padayatti, P.S. / Helfand, M.S. / Carey, M.P. / Bonomo, R.A. / Carey, P.R. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h0t.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h0t.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h0t_validation.pdf.gz | 873.4 KB | Display | wwPDB validaton report |
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Full document | 2h0t_full_validation.pdf.gz | 877 KB | Display | |
Data in XML | 2h0t_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2h0t_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0t ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0t | HTTPS FTP |
-Related structure data
Related structure data | 2h0yC 2h10C 1rcjS 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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Details | Protein is a monomer |
-Components
#1: Protein | Mass: 28816.920 Da / Num. of mol.: 1 / Fragment: SHV-1 b-lactamase / Mutation: M69V, E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaSHV-1, SHV-1b-a, blaSHV-11 / Production host: Escherichia coli (E. coli) References: UniProt: Q5PSW7, UniProt: P0AD64*PLUS, beta-lactamase | ||||
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#2: Chemical | ChemComp-TEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: 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: 1.99 Å3/Da / Density % sol: 38.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 6000, 0.1M HEPES pH 7.0, 0.56mM Cymal-6. Crystal is soaked for 10 minutes in 50mM clavulanic acid prior to freezing and data collection., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.46 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Sep 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.46 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.91 Å / Num. obs: 31000 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.506 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RCJ Resolution: 1.6→18.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1331953.67 / Data cutoff high rms absF: 1331953.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.2699 Å2 / ksol: 0.454706 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→18.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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