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Open data
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Basic information
Entry | Database: PDB / ID: 1e4d | ||||||
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Title | Structure of OXA10 beta-lactamase at pH 8.3 | ||||||
![]() | BETA-LACTAMASE OXA-10 | ||||||
![]() | BETA-LACTAMASE / ANTIOBITIC RESISTANCE | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 417.1 KB | Display | ![]() |
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PDB format | ![]() | 342.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.6 KB | Display | ![]() |
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Full document | ![]() | 485.9 KB | Display | |
Data in XML | ![]() | 48.3 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e3uSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |