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Yorodumi- PDB-1ero: X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ero | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-2-PHENYLACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL BORONIC ACID | ||||||
Components | TEM-1 BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / beta-lactamase / structure-based design / boronate inhibitor | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Ness, S. / Martin, R. / Kindler, A.M. / Paetzel, M. / Gold, M. / Jones, J.B. / Strynadka, N.C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase(,). Authors: Ness, S. / Martin, R. / Kindler, A.M. / Paetzel, M. / Gold, M. / Jensen, S.E. / Jones, J.B. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ero.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ero.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ero.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ero_validation.pdf.gz | 488.5 KB | Display | wwPDB validaton report |
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Full document | 1ero_full_validation.pdf.gz | 500.5 KB | Display | |
Data in XML | 1ero_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1ero_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/1ero ftp://data.pdbj.org/pub/pdb/validation_reports/er/1ero | HTTPS FTP |
-Related 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: 28941.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
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#2: Chemical | ChemComp-BJP / ( |
#3: 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: 1.99 Å3/Da / Density % sol: 38.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 1.5 M / Common name: phosphate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 2, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 39379 / Num. obs: 14567 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 46.6 |
Reflection shell | Resolution: 2.07→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.163 / Num. unique all: 1262 / % possible all: 80.4 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 18128 / Num. measured all: 73805 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 Stereochemistry target values: bond length = 1.0 bond angle = 1.5 Try planes = 1.2 Gen planes = 4.0 bad contacts 12.0 Temp. = 3.0
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0 / Rfactor all: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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