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- PDB-6zrj: Crystal structure of class D Beta-lactamase OXA-48 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zrj | ||||||
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Title | Crystal structure of class D Beta-lactamase OXA-48 in complex with ertapenem | ||||||
![]() | (Beta-lactamase) x 2 | ||||||
![]() | HYDROLASE / Beta-lactamase / CHDL / OXA-48 / carbapenem / ertapenem / acylenzyme | ||||||
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 | ![]() | 445 KB | Display | ![]() |
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PDB format | ![]() | 361.2 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 ![]() 6zrhC ![]() 6zriC ![]() 6zrpC ![]() 6zw2C ![]() 3hbrS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ACDEFGHB
#1: Protein | Mass: 30439.725 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 30396.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462 Plasmid: pET-9a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 1657 molecules ![](data/chem/img/2RG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-2RG / ( #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG 4000, 5-8% 1-butanol, and 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 27, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→48.51 Å / Num. obs: 157924 / % possible obs: 97.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.055 / Rrim(I) all: 0.099 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.94→2.04 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 22664 / CC1/2: 0.719 / Rpim(I) all: 0.385 / Rrim(I) all: 0.667 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HBR Resolution: 1.94→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.982 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.163 / 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: 109.12 Å2 / Biso mean: 28.921 Å2 / Biso min: 5.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2337 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→48.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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