+Open data
-Basic information
Entry | Database: PDB / ID: 3bls | ||||||
---|---|---|---|---|---|---|---|
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 SUBSTITUTION / Resolution: 2.3 Å | ||||||
Authors | Usher, K.C. / Shoichet, B.K. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bls.cif.gz | 146 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bls.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bls_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bls_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 3bls_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 3bls_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bls ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bls | HTTPS FTP |
-Related structure data
Related structure data | 2blsSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99824, 0.058222, -0.011253), 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: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.7 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M NA/K PHOSPHATE, PH 8.7, COCRYSTALLIZED IN THE PRESENCE OF MAPB INHIBITOR. 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
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 1, 1995 / 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: 2.3→25 Å / Num. obs: 35225 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.3→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3 |
Reflection | *PLUS Num. all: 36886 / Num. measured all: 114023 |
Reflection shell | *PLUS % possible obs: 88.3 % / Num. possible: 7324 / Num. unique obs: 6468 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR SUBSTITUTION Starting model: PDB ENTRY 2BLS Resolution: 2.3→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET SCALING / Bsol: 531 Å2 / ksol: 0.99 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|