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Yorodumi- PDB-5bo2: Bianthranilate-like inhibitor with 4-atom "line" and phosphonate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bo2 | |||||||||
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Title | Bianthranilate-like inhibitor with 4-atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD) | |||||||||
Components | Anthranilate phosphoribosyltransferase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Lobenzarit-like analogue / TB Structural Genomics Consortium / TBSGC / magnesium binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Evans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: To be Published Title: Binding and mimicking of the phosphate-rich substrate, PRPP. Authors: Evans, G.L. / Baker, E.N. / Lott, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bo2.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bo2.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5bo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/5bo2 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bo2 | HTTPS FTP |
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-Related structure data
Related structure data | 5bneC 5bo3C 5bytC 5c1rC 3qr9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38948.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: trpD, MRA_2208 / Plasmid: pET23A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41(DE3)pLysS References: UniProt: A5U4M0, anthranilate phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-IMD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.2 % / Description: Flat-diamond shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole-malate, 9% PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→47 Å / Num. obs: 47170 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.5 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3QR9 chain A Resolution: 2→46.963 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.56 / 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: 2→46.963 Å
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Refine LS restraints |
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LS refinement shell |
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