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Open data
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Basic information
Entry | Database: PDB / ID: 6zrh | ||||||
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Title | Crystal structure of OXA-10loop24 in complex with ertapenem | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Beta-lactamase / OXA-10loop24 / carbapenem / ertapenem / acylenzyme / laboratory variant | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassone, G. / Di Pisa, F. / Benvenuti, M. / De Luca, F. / Pozzi, C. / Mangani, S. / Docquier, J.D. | ||||||
![]() | ![]() Title: Mechanistic insights into carbapenem hydrolysis by OXA-48 and the OXA10-derived hybrids OXA-10 loop24 and loop48 Authors: Tassone, G. / Di Pisa, F. / Benvenuti, M. / De Luca, F. / Pozzi, C. / Mangani, S. / Docquier, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.5 KB | Display | ![]() |
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PDB format | ![]() | 186 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zrgC ![]() 6zriC ![]() 6zrjC ![]() 6zrpC ![]() 6zw2C ![]() 3qnbS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 27377.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: blaoxa-10, blaOXA-10, oxa-10, BK373_28375, CQP61_30695, E4K55_27185, FORC82_p097, GII67_09965 Plasmid: pLBII / Production host: ![]() ![]() #2: Chemical | ChemComp-2RG / ( #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.6 - 3 M ammonium sulfate and 100 mM TRIS, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→35.73 Å / Num. obs: 82741 / % possible obs: 91.2 % / Redundancy: 3 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.076 / Rrim(I) all: 0.143 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12261 / CC1/2: 0.781 / Rpim(I) all: 0.282 / Rrim(I) all: 0.538 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QNB Resolution: 1.88→35.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.258 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.98 Å2 / Biso mean: 20.342 Å2 / Biso min: 7.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1903 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.88→35.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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