+Open data
-Basic information
Entry | Database: PDB / ID: 1m40 | |||||||||
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Title | ULTRA HIGH RESOLUTION CRYSTAL STRUCTURE OF TEM-1 | |||||||||
Components | BETA-LACTAMASE TEM | |||||||||
Keywords | HYDROLASE / BETA-LACTAMASE / ACYLATION MECHANISM | |||||||||
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: 0.85 Å | |||||||||
Authors | Minasov, G. / Wang, X. / Shoichet, B.K. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation. Authors: Minasov, G. / Wang, X. / Shoichet, B.K. | |||||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE NUMBERING IS NOT SEQUENTIAL. NUMBERS 239 AND 253 ARE NOT USED IN THE COORDINATES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m40.cif.gz | 244.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m40.ent.gz | 212.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m40 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m40 | HTTPS FTP |
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-Related structure data
Related structure data | 1jwpS 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: 28911.904 Da / Num. of mol.: 1 / Mutation: M182T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II - TEM-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: UniProt: P62593, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-CB4 / | #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: 1.97 Å3/Da / Density % sol: 37.43 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium-potassium buffer, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion / 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: 0.7999 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 7, 2001 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→15 Å / Num. all: 200302 / Num. obs: 200302 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 0.85→0.87 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / Num. unique all: 13237 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 1143489 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 13237 / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JWP Resolution: 0.85→10 Å / Num. parameters: 36034 / Num. restraintsaints: 76566 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM USED IN REFINEMENT
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Displacement parameters | Biso mean: 12.2 Å2
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Refine analyze | Num. disordered residues: 448 / Occupancy sum hydrogen: 1684 / Occupancy sum non hydrogen: 2507.95 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.85→0.878 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.1117 / Rfactor Rwork: 0.091 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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