+Open data
-Basic information
Entry | Database: PDB / ID: 1e3u | ||||||
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Title | MAD structure of OXA10 class D beta-lactamase | ||||||
Components | (BETA-LACTAMASE OXA- ...) x 2 | ||||||
Keywords | BETA-LACTAMASE / ANTIOBITIC RESISTANCE | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å | ||||||
Authors | Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Insights Into Class D Beta-Lactamases are Revealed by the Crystal Structure of the Oxa10 Enzyme from Pseudomonas Aeruginosa Authors: Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / 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 | 1e3u.cif.gz | 407.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3u.ent.gz | 347 KB | Display | PDB format |
PDBx/mmJSON format | 1e3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3u ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-BETA-LACTAMASE OXA- ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 27524.291 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Cellular location (production host): EXCRETED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase #2: Protein | | Mass: 27506.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Cellular location (production host): EXCRETED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase |
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-Non-polymers , 4 types, 984 molecules
#3: Chemical | ChemComp-AUC / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: 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: 2.49 Å3/Da / Density % sol: 0.561 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.2 Details: AMMONIUMS SULFATE 2.0 M, TRIS HCL 100 MM, PH 8.2-8.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95375, 1.0376 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000 / Details: COLLIMATOR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.653→43.1 Å / Num. obs: 127968 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.315 Å2 / Rsym value: 0.064 / Net I/σ(I): 8.1 | |||||||||
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.322 / % possible all: 93.4 | |||||||||
Reflection | *PLUS Num. measured all: 598857 / Rmerge(I) obs: 0.064 | |||||||||
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.66→40 Å / SU B: 1.02065 / SU ML: 0.03474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14003 / ESU R Free: 0.09546 / Details: INDIVIDUAL ANISOTROPIC B FACTORS WERE REFINED
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Displacement parameters | Biso mean: 19.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1806 / Rfactor Rfree: 0.20966 / Rfactor Rwork: 0.18057 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |