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- PDB-6zrg: Crystal structure of OXA-10loop48 in complex with hydrolyzed doripenem -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zrg | ||||||
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Title | Crystal structure of OXA-10loop48 in complex with hydrolyzed doripenem | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Beta-lactamase / OXA-10loop48 / carbapenem / doripenem | ||||||
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. / Docquier, J.D. / Mangani, S. | ||||||
![]() | ![]() 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. / Docquier, J.D. / Mangani, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 96.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.1 KB | Display | ![]() |
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Full document | ![]() | 756.6 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zrhC ![]() 6zriC ![]() 6zrjC ![]() 6zrpC ![]() 6zw2C ![]() 3qncS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27568.412 Da / Num. of mol.: 2 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: pET-24 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 558 molecules ![](data/chem/img/QP2.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-QP2 / ( | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 2.6 - 3 M ammonium sulfate and 100 mM bicine, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→52.39 Å / Num. obs: 61062 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8793 / CC1/2: 0.862 / Rpim(I) all: 0.276 / Rrim(I) all: 0.65 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QNC Resolution: 1.74→52.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.828 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.109 / 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: 77.1 Å2 / Biso mean: 25.023 Å2 / Biso min: 9.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2009 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→52.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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