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Yorodumi- PDB-5nj2: Crystal structure of BlaC from Mycobacterium tuberculosis bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nj2 | ||||||
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Title | Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Tassoni, R. / Pannu, N.S. / Ubbink, M. | ||||||
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 | 5nj2.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nj2.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/5nj2 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/5nj2 | HTTPS FTP |
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-Related structure data
Related structure data | 5oyoC 2gdnS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 30 - 293 / Label seq-ID: 3 - 265
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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.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0T9EA39, UniProt: P9WKD3*PLUS, beta-lactamase |
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-Non-polymers , 5 types, 297 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-ETE / | #5: Chemical | ChemComp-AE4 / | #6: 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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate buffer, pH 5.0, 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→75.36 Å / Num. obs: 96841 / % possible obs: 62.7 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.041 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.19→1.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 689 / CC1/2: 0.523 / Rpim(I) all: 0.467 |
-Processing
Software | Name: REFMAC / Version: 7.0.033 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDN Resolution: 1.19→75.36 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.829 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / 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: 11.803 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→75.36 Å
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Refine LS restraints |
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