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Yorodumi- PDB-4ij1: Bianthranilate-like analogue bound to anthranilate phosphoribosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ij1 | ||||||
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Title | Bianthranilate-like analogue bound to anthranilate phosphoribosyltransferase (AnPRT; trpD) in absence of substrates. | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor complex / bi-anthranilate analogue / TB Structural Genomics Consortium / TBSGC / phosphoribosyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Evans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis in Mycobacterium tuberculosis. Authors: Evans, G.L. / Gamage, S.A. / Bulloch, E.M. / Baker, E.N. / Denny, W.A. / 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 | 4ij1.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ij1.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ij1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ij1 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ij1 | HTTPS FTP |
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-Related structure data
Related structure data | 4giuC 4gkmC 4m0rC 3qr9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39086.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2248, MTCY190.03c, Rv2192c, trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pGroESL References: UniProt: P66992, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase #2: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M imidazole.malate, 15% PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.8983 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8983 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.594→95.201 Å / Num. obs: 65430 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.504 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.172 / Net I/σ(I): 6.71 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QR9 CHAIN A Resolution: 1.79→47.601 Å / SU ML: 0.24 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.52 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→47.601 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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