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Yorodumi- PDB-4qb8: Crystal Structure of beta-lactamase from M.tuberculosis forming M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qb8 | ||||||
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Title | Crystal Structure of beta-lactamase from M.tuberculosis forming Michaelis Menten with Tebipenem | ||||||
Components | Beta-lactamase | ||||||
Keywords | hydrolase/antibiotic / 3-Layer Sandwich / DD-peptidase/beta-lactamase superfamily / tebipenem pivoxil / carbapenem / destroying betalactam antibiotics / hydrolase-antibiotic complex | ||||||
Function / homology | Function and homology information penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.758 Å | ||||||
Authors | Hazra, S. / Blanchard, J. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Tebipenem, a new carbapenem antibiotic, is a slow substrate that inhibits the beta-lactamase from Mycobacterium tuberculosis. Authors: Hazra, S. / Xu, H. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qb8.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qb8.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/4qb8 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/4qb8 | HTTPS FTP |
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-Related 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: 28356.777 Da / Num. of mol.: 1 / Fragment: unp residues 42-307 / Mutation: K73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: blaA, blaC, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKD3, beta-lactamase | ||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-1TE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.53 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, pH 7.5, 2M NH4H2PO4 Protein concentration 12 mgs/ml, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→23.5 Å / Num. all: 25499 / Num. obs: 25431 / % possible obs: 97.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.758→23.475 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 16.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.758→23.475 Å
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Refine LS restraints |
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LS refinement shell |
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