+Open data
-Basic information
Entry | Database: PDB / ID: 1li0 | ||||||
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Title | Crystal structure of TEM-32 beta-Lactamase at 1.6 Angstrom | ||||||
Components | Class A beta-Lactamase- TEM-32 | ||||||
Keywords | HYDROLASE / beta-Lactamase / antibiotic resistance / TEM-32 | ||||||
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: 1.61 Å | ||||||
Authors | Wang, X. / Minasov, G. / Shoichet, B.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34. Authors: Wang, X. / Minasov, G. / 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 | 1li0.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1li0.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 1li0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1li0_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 1li0_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 1li0_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1li0_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1li0 ftp://data.pdbj.org/pub/pdb/validation_reports/li/1li0 | HTTPS FTP |
-Related structure data
Related structure data | 1lhyC 1li9C 1jwpS 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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Unit cell |
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-Components
#1: Protein | Mass: 28893.865 Da / Num. of mol.: 1 / Mutation: M69I, M182T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: UniProt: P62593, beta-lactamase | ||
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#2: Chemical | ChemComp-BCT / | ||
#3: Chemical | #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: 1.91 Å3/Da / Density % sol: 35.72 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium-potassium buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: used seeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Dec 19, 2001 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→17 Å / Num. all: 29385 / Num. obs: 29385 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2931 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 17 Å / Num. measured all: 181694 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1JWP Resolution: 1.61→17 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Crystallographic conjugate gradient minimization refinement using maximum likelihood target for amplitudes
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Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.61→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.67 Å
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Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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