+Open data
-Basic information
Entry | Database: PDB / ID: 1e4d | ||||||
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Title | Structure of OXA10 beta-lactamase at pH 8.3 | ||||||
Components | BETA-LACTAMASE OXA-10 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 1e4d.cif.gz | 417.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e4d.ent.gz | 342.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e4d ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e4d | HTTPS FTP |
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-Related structure data
Related structure data | 1e3uSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 27567.293 Da / Num. of mol.: 4 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: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: 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: 2.53 Å3/Da / Density % sol: 0.561 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.3 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: ESRF / Beamline: BM30A / Wavelength: 0.9796 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.54 Å / Num. obs: 86153 / % possible obs: 84.4 % / Redundancy: 3 % / Biso Wilson estimate: 22.19 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.331 / % possible all: 90.7 |
Reflection | *PLUS Num. measured all: 258171 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 91.1 % / Rmerge(I) obs: 0.331 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E3U Resolution: 1.8→29.54 Å / SU B: 1.95692 / SU ML: 0.06092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.86904 / ESU R Free: 0.15506 Details: INDIVIDUAL ANISOTROPIC BFACTORS WERE REFINED. THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
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Displacement parameters | Biso mean: 22.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.54 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1983 / Rfactor Rfree: 0.24271 / Rfactor Rwork: 0.19831 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |