+Open data
-Basic information
Entry | Database: PDB / ID: 1g6a | ||||||
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Title | PSE-4 CARBENICILLINASE, R234K MUTANT | ||||||
Components | BETA-LACTAMASE PSE-4 | ||||||
Keywords | HYDROLASE / class A beta-lactamase / carbenicillinase / R234K mutant | ||||||
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 / direct refinement / Resolution: 1.75 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g6a.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g6a.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g6a_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 1g6a_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 1g6a_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1g6a_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6a ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6a | HTTPS FTP |
-Related structure data
Related structure data | 1g68SC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29528.158 Da / Num. of mol.: 1 / Mutation: R234K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / 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: 2.4 Å3/Da / Density % sol: 48.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: ammonium sulfate, sodium acetate, pH 4.5, 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: Aug 13, 2000 / 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: 1.75→25 Å / Num. all: 29406 / Num. obs: 29406 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2831 / % possible all: 98.6 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 162602 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: direct refinement Starting model: PSE-4 wild type structure (1G68) Resolution: 1.75→23.05 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1748067.93 / 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: 59.79 Å2 / ksol: 0.4137 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→23.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 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: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.249 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.242 |