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- PDB-7b3r: OXA-10 beta-lactamase with S64Dha modification and lysinoalanine ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b3r | ||||||
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Title | OXA-10 beta-lactamase with S64Dha modification and lysinoalanine crosslink | ||||||
![]() | (Beta-lactamase OXA-10) x 2 | ||||||
![]() | HYDROLASE / beta lactamase / antibiotic resistance / tazobactam / dehydroalanine / irreversible inhibition / covalent modification | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lang, P.A. / Brem, J. / Schofield, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Studies on enmetazobactam clarify mechanisms of widely used beta-lactamase inhibitors. Authors: Lang, P.A. / Raj, R. / Tumber, A. / Lohans, C.T. / Rabe, P. / Robinson, C.V. / Brem, J. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.4 KB | Display | ![]() |
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PDB format | ![]() | 166.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.6 KB | Display | ![]() |
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Full document | ![]() | 434.3 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t35C ![]() 7b3sC ![]() 7b3uC ![]() 1k55S 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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Unit cell |
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Components
#1: Protein | Mass: 27680.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 27637.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→63.093 Å / Num. obs: 52627 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.053 / Rrim(I) all: 0.19 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K55 Resolution: 1.83→63.09 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.3 Å2 / Biso mean: 32.7061 Å2 / Biso min: 13.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→63.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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