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- PDB-8btv: Structure of D179N BlaC from Mycobacterium tuberculosis bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8btv | ||||||
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Title | Structure of D179N BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of sulbactam | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chikunova, A. / Bruenle, S. / Ubbink, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Asp179 in the class A beta-lactamase from Mycobacterium tuberculosis is a conserved yet not essential residue due to epistasis. Authors: van Alen, I. / Chikunova, A. / van Zanten, D.B. / de Block, A.A. / Timmer, M. / Brunle, 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 | ![]() | 70.3 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 741.7 KB | Display | ![]() |
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Full document | ![]() | 743.3 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8btuC ![]() 8btwC ![]() 8bv4C ![]() 6h2kS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28328.789 Da / Num. of mol.: 1 / Mutation: D179N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: blaC, blaA, MT2128 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-TSL / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium phosphate/citrate (pH 5.5); 20% v/v PEGSH |
-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: Dec 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→53.87 Å / Num. obs: 17094 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.989 / Rpim(I) all: 0.085 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.93→1.98 Å / Num. unique obs: 1184 / CC1/2: 0.683 / Rpim(I) all: 0.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6H2K Resolution: 1.95→53.87 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.309 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.684 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→53.87 Å
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Refine LS restraints |
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