+Open data
-Basic information
Entry | Database: PDB / ID: 5hvi | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of TEM1 beta-lactamase | |||||||||
Components | Beta-lactamase TEM | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Roose, B.W. / Dmochowski, I.J. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Chemphyschem / Year: 2018 Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase. Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hvi.cif.gz | 413.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hvi.ent.gz | 335.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hvi_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5hvi_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 5hvi_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 5hvi_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hvi ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hvi | HTTPS FTP |
-Related structure data
Related structure data | 5hw1C 5i52C 5i63C 5kkfC 5kpuC 6apaC 6aykC 1btlS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28911.904 Da / Num. of mol.: 4 / Mutation: M180T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.77 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 2% (v/v) tacsimate (pH 6.0), 0.1 M Bis-Tris (pH 6.5), 20% (w/v) PEG 3350 PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Dec 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.02 |
Reflection | Resolution: 1.64→63.2 Å / Num. obs: 113836 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.037 / Net I/σ(I): 15.1 / Num. measured all: 409738 / Scaling rejects: 276 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.4 / % possible all: 89.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BTL Resolution: 1.64→63.198 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.83
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.22 Å2 / Biso mean: 12.2983 Å2 / Biso min: 3.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.64→63.198 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|