+Open data
-Basic information
Entry | Database: PDB / ID: 1vm1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM | |||||||||
Components | BETA-LACTAMASE SHV-1 | |||||||||
Keywords | HYDROLASE / Beta-LACTAMASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT Binding / Inhibitor design | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam. Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R. #1: Journal: Biochemistry / Year: 1999 Title: Structure of the SHV-1 Beta-Lactamase Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1vm1.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1vm1.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vm1_validation.pdf.gz | 657.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1vm1_full_validation.pdf.gz | 632.2 KB | Display | |
Data in XML | 1vm1_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1vm1_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vm1 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vm1 | HTTPS FTP |
-Related structure data
Related structure data | 1shvS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28907.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BLA / Plasmid: PBCSK / Species (production host): Escherichia coli Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) Strain (production host): DH10B References: UniProt: Q9F643, UniProt: P0AD64*PLUS, beta-lactamase |
---|
-Non-polymers , 5 types, 180 molecules
#2: Chemical | #3: Chemical | ChemComp-TBE / | #4: Chemical | ChemComp-AKR / | #5: Chemical | ChemComp-TAZ / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% PEG-6000, 50 mM HEPES, 0.56 mM Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.54 Å | |||||||||
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 1, 1999 / Details: MIRRORS | |||||||||
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.02→50 Å / Num. all: 14540 / Num. obs: 13813 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.077 / Net I/σ(I): 12.1 | |||||||||
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1843 / Rsym value: 0.26 / % possible all: 72 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SHV Resolution: 2.02→50 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| |||||||||||||||||||||||||
Xplor file |
|