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- PDB-6h2c: Structure of BlaC from Mycobacterium tuberculosis bound to the tr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h2c | ||||||
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Title | Structure of BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct derived from clavulanic acid. | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassoni, R. / Pannu, N.S. / Ubbink, M. | ||||||
![]() | ![]() Title: New Conformations of Acylation Adducts of Inhibitors of beta-Lactamase from Mycobacterium tuberculosis. Authors: Tassoni, R. / Blok, A. / Pannu, N.S. / Ubbink, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.1 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823.6 KB | Display | ![]() |
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Full document | ![]() | 830.7 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h27C ![]() 6h28C ![]() 6h2aC ![]() 6h2gC ![]() 6h2hC ![]() 6h2iC ![]() 6h2kC ![]() 2gdnS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 28 - 295 / Label seq-ID: 1 - 268
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29475.061 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0T9EA39, UniProt: A0A655AHQ9*PLUS, beta-lactamase |
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-Non-polymers , 6 types, 122 molecules ![](data/chem/img/ISS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Chemical | ChemComp-CO2 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 5.0 25% w/v PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→41.12 Å / Num. obs: 34426 / % possible obs: 94.4 % / Redundancy: 2.3 % / CC1/2: 0.974 / Rpim(I) all: 0.124 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3078 / CC1/2: 0.709 / Rpim(I) all: 0.342 / % possible all: 85.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GDN Resolution: 1.93→41.12 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 7.015 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.358 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→41.12 Å
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Refine LS restraints |
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