+Open data
-Basic information
Entry | Database: PDB / ID: 2bls | ||||||
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Title | AMPC BETA-LACTAMASE FROM ESCHERICHIA COLI | ||||||
Components | AMPC BETA-LACTAMASE | ||||||
Keywords | CEPHALOSPORINASE / BETA-LACTAMASE / SERINE HYDROLASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Usher, K.C. / Wery, J.-P. / Blaszczak, L.C. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design. Authors: Usher, K.C. / Blaszczak, L.C. / Weston, G.S. / Shoichet, B.K. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bls.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bls.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2bls ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2bls | HTTPS FTP |
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-Related structure data
Related structure data | 3blsC 2blt S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997453, 0.070717, 0.00935), Vector: |
-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASM / Gene: AMPC / Plasmid: POG0295 / Cellular location (production host): EXTRACELLULAR / Gene (production host): AMPC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||
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Crystal grow | pH: 8.7 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M NA/K PHOSPHATE, PH 8.7. LARGER CRYSTALS WERE GROWN BY MICRO-SEEDING TECHNIQUE | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 8.7 / PH range high: 8.5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 41301 / % possible obs: 77.4 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2→2.25 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 3.1 / % possible all: 58.1 |
Reflection | *PLUS Num. all: 52822 / Num. measured all: 73349 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 58.1 % / Num. possible: 15650 / Num. unique obs: 9094 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BLT 2blt Resolution: 2→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 1 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 149 Å2 / ksol: 0.87 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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