+Open data
-Basic information
Entry | Database: PDB / ID: 1g68 | ||||||
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Title | PSE-4 CARBENICILLINASE, WILD TYPE | ||||||
Components | BETA-LACTAMASE PSE-4 | ||||||
Keywords | HYDROLASE / class A beta-lactamase / carbenicillinase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Lim, D. / Sanschagrin, F. / Passmore, L. / De Castro, L. / Levesque, R.C. / Strynadka, N.C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies. Authors: Lim, D. / Sanschagrin, F. / Passmore, L. / De Castro, L. / Levesque, R.C. / Strynadka, N.C. | ||||||
History |
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Remark 999 | SEQUENCE THE RESIDUE NUMBERING IN NOT SEQUENTIAL. RESIDUES 57 AND 59, 238 AND 240, 252 AND 254 ARE ...SEQUENCE THE RESIDUE NUMBERING IN NOT SEQUENTIAL. RESIDUES 57 AND 59, 238 AND 240, 252 AND 254 ARE COVALENTLY BOUND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g68.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g68.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g68 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g68 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29556.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PSE4 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMDADE3 / References: UniProt: P16897, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.41 Å3/Da / Density % sol: 48.88 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, MgCl2, MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 28, 1999 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. all: 21494 / Num. obs: 21494 / % possible obs: 99.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.219 / Num. unique all: 2035 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 208439 |
Reflection shell | *PLUS % possible obs: 96.5 % / Mean I/σ(I) obs: 8.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TEM-1 native structure Resolution: 1.95→24.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2038344.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.96 Å2 / ksol: 0.4186 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→24.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.222 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.175 |