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Yorodumi- PDB-7a72: Structure of G132S BlaC from Mycobacterium tuberculosis bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a72 | |||||||||
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Title | Structure of G132S BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of sulbactam | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / BlaC / beta-lactamase / Mycobacterium tuberculosis / inhibitor | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Chikunova, A. / Ahmad, M.U. / Perrakis, A. / Ubbink, M. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: Biochemistry / Year: 2021 Title: The G132S Mutation Enhances the Resistance of Mycobacterium tuberculosis beta-Lactamase against Sulbactam. Authors: van Alen, I. / Chikunova, A. / Safeer, A.A. / Ahmad, M.U.D. / Perrakis, A. / Ubbink, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a72.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a72.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 7a72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a72_validation.pdf.gz | 355 KB | Display | wwPDB validaton report |
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Full document | 7a72_full_validation.pdf.gz | 355.6 KB | Display | |
Data in XML | 7a72_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7a72_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/7a72 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/7a72 | HTTPS FTP |
-Related structure data
Related structure data | 7a5tC 7a5wC 7a71C 6h2kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28359.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655AHQ9, beta-lactamase | ||||||
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#2: Chemical | ChemComp-TSL / | ||||||
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 0.1 M Sodium Cacodylate, 15% PEG-SB, 10% Ethylene Glycol, 5% TMate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.912 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→78.2 Å / Num. obs: 56098 / % possible obs: 98.2 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2775 / CC1/2: 0.655 / Rpim(I) all: 0.582 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H2K Resolution: 1.3→44.84 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.436 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / 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: 14.333 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→44.84 Å
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Refine LS restraints |
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