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Open data
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Basic information
Entry | Database: PDB / ID: 6pq9 | ||||||
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Title | Crystal Structure of TLA-1 S70G extended spectrum Beta-lactamase | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Lactamase / Antibiotic / Resistance / HIDROLASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rudino-Pinera, E. / Cifuentes-Castro, V.H. / Rodriguez-Alamazan, C. | ||||||
![]() | ![]() Title: The crystal structure of ESBL TLA-1 in complex with clavulanic acid reveals a second acylation site. Authors: Cifuentes-Castro, V. / Rodriguez-Almazan, C. / Silva-Sanchez, J. / Rudino-Pinera, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 298.7 KB | Display | ![]() |
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Full document | ![]() | 298.5 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nvtC ![]() 6nvuSC ![]() 6pq8C 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33342.285 Da / Num. of mol.: 1 / Mutation: S70G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 196 molecules ![](data/chem/img/ASP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ASP / | ||||||
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#3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.05 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2.4 M Ammonium Sulfate, 100 mM Sodium Phosphate dibasic/ Citric acid pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2018 / Details: Sagitally focusing 2nd crystal |
Radiation | Monochromator: Si (111) Rosenbaum-Rock double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793326 Å / Relative weight: 1 |
Reflection | Resolution: 2.191→19.89 Å / Num. obs: 26170 / % possible obs: 99.9 % / Redundancy: 10.74 % / Biso Wilson estimate: 41.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.084 / Rsym value: 0.084 / Net I/σ(I): 30.14 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 1.12 / Num. unique obs: 3202 / CC1/2: 0.898 / Rrim(I) all: 1.15 / Rsym value: 1.16 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NVU Resolution: 2.191→19.89 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.89 Å2 / Biso mean: 44.1204 Å2 / Biso min: 25.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.191→19.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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