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Yorodumi- PDB-4m0r: Trianthranilate-like analogue bound to anthranilate phosphoribosy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m0r | ||||||
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Title | Trianthranilate-like analogue bound to anthranilate phosphoribosyltransferase (AnPRT; TrpD). | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Magnesium binding / phosphoribosylpyrophosphate / PRPP / inhibitor complex / tri-anthranilate analogue / TB Structural Genomics Consortium / TBSGC / phosphoribosyltransferase / transferase / 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: 1.96 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 | 4m0r.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m0r.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m0r_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4m0r_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4m0r_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4m0r_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m0r ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m0r | HTTPS FTP |
-Related structure data
Related structure data | 4giuC 4gkmC 4ij1C 3qr9S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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: 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 |
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-Non-polymers , 5 types, 349 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-IMD / | #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: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M imidazole.malate, 11% PEG-4000, pH 7.5, 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: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2012 |
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→91.76 Å / Num. all: 63534 / Num. obs: 63134 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 25.052 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2 / Num. unique all: 9117 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CHAIN A OF PDB ENTRY 3QR9 Resolution: 1.96→60.079 Å / SU ML: 0.25 / Isotropic thermal model: Isotropic & Anisotropic / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.617 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→60.079 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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