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- PDB-1k54: OXA-10 class D beta-lactamase partially acylated with reacted 6be... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k54 | ||||||
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Title | OXA-10 class D beta-lactamase partially acylated with reacted 6beta-(1-hydroxy-1-methylethyl) penicillanic acid | ||||||
![]() | (Beta lactamase OXA- ...) x 2 | ||||||
![]() | HYDROLASE / beta-lactamase / antibiotic resistance / carbamylation | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S. | ||||||
![]() | ![]() Title: Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S. #1: ![]() 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. #2: ![]() Title: The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotic Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, 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 | ![]() | 402.9 KB | Display | ![]() |
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PDB format | ![]() | 327.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 66.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k55C ![]() 1k56C ![]() 1k57C ![]() 1e4dS 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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Details | the biological assembly is a dimer. There are two dimers in the asymmetric unit : chains A and C form a dimer chains B and D form a dimer |
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Components
-Beta lactamase OXA- ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 27567.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residue 70 is KCX, carbamylated lysine. Acylated at SER 67. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 27524.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 846 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOQ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOQ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: 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: 51.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulafate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 | ||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000 |
Radiation | Monochromator: diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.77 Å / Num. all: 119631 / Num. obs: 119631 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.115 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.2 / Num. unique all: 16474 / Rsym value: 0.289 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 432971 |
Reflection shell | *PLUS % possible obs: 93.8 % / Num. unique obs: 16474 / Num. measured obs: 45364 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1e4d Resolution: 1.7→44.77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
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Displacement parameters | Biso mean: 16.799 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→44.77 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.7 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.225 / Total num. of bins used: 20 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 1.5 % / Rfactor obs: 0.17688 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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