+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+25 | ||||||
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Title | The high resolution structure of PER-1 class A beta-lactamase | ||||||
Components | EXTENDED-SPECTRUM BETA-LACTAMASE PER-1 | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CEPHALOSPORINASE | ||||||
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 / SYNCHROTRON / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Tranier, S. / Bouthors, A.T. / Maveyraud, L. / Guillet, V. / Sougakoff, W. / Samama, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The High Resolution Crystal Structure for Class a Beta-Lactamase Per-1 Reveals the Bases for its Increase in Breadth of Activity Authors: Tranier, S. / Bouthors, A.T. / Maveyraud, L. / Guillet, V. / Sougakoff, W. / Samama, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e25.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e25.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 1e25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e25_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 1e25_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 1e25_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1e25_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e25 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e25 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30945.529 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: RNL-1 / Gene: BLAPER-1 / Plasmid: PK19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P37321, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: 18% (V/V) SATURATED AMMONIUM SULFATE, 1MM DITHIOTHREITOL, 100 MM SODIUM ACETATE, PH4.7, pH 4.70 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / pH: 7.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.18 Å / Num. obs: 25029 / % possible obs: 94.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.122 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 66657 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.122 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1509650.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE 3 C-TERMINAL RESIDUES AND THE FIRST N-TERMINAL RESIDUE WERE NOT SEEN IN THE DENSITY MAPS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0192 Å2 / ksol: 0.364363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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