+Open data
-Basic information
Entry | Database: PDB / ID: 5oyo | ||||||
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Title | Crystal structure of BlaC from Mycobacterium tuberculosis | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information : / : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tassoni, R. / Pannu, N.S. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Phosphate Promotes the Recovery of Mycobacterium tuberculosis beta-Lactamase from Clavulanic Acid Inhibition. Authors: Elings, W. / Tassoni, R. / van der Schoot, S.A. / Luu, W. / Kynast, J.P. / Dai, L. / Blok, A.J. / Timmer, M. / Florea, B.I. / Pannu, N.S. / Ubbink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oyo.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oyo.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 5oyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oyo ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oyo | HTTPS FTP |
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-Related structure data
Related structure data | 5nj2C 2gdnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 29 - 294 / Label seq-ID: 2 - 267
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-Components
#1: Protein | Mass: 29475.061 Da / Num. of mol.: 2 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: A0A0T9EA39, UniProt: P9WKD3*PLUS, beta-lactamase #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 5.0, 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96773 Å |
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: 0.96773 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40.13 Å / Num. obs: 33346 / % possible obs: 94.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.074 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2851 / Rpim(I) all: 0.572 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDN Resolution: 2.1→40.13 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.823 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.222 / 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: 19.828 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→40.13 Å
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Refine LS restraints |
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