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Yorodumi- PDB-1kvm: X-ray Crystal Structure of AmpC WT beta-Lactamase in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kvm | ||||||
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Title | X-ray Crystal Structure of AmpC WT beta-Lactamase in Complex with Covalently Bound Cephalothin | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / amide hydrolase / beta-lactamase / cephalothin / acyl-enzyme complex | ||||||
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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Authors: Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kvm.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvm.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kvm_validation.pdf.gz | 775.4 KB | Display | wwPDB validaton report |
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Full document | 1kvm_full_validation.pdf.gz | 783.9 KB | Display | |
Data in XML | 1kvm_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1kvm_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvm ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvm | HTTPS FTP |
-Related structure data
Related structure data | 1kvlC 1fsyS 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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Unit cell |
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-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-CEO / | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.51 Å3/Da / Density % sol: 51.06 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate, then crystal soaked with saturated cephalothin solution in crystallizing buffer for 2x 15 minutes, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Temperature: 23 ℃ |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate / Details: pH8.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→20 Å / Num. obs: 46729 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.06→2.11 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.93 / % possible all: 83.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 168893 |
Reflection shell | *PLUS % possible obs: 83.4 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FSY Resolution: 2.06→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.13 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.176 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.11 Å |