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Yorodumi- PDB-4gkm: Bianthranilate-like analogue bound in the outer site of anthranil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gkm | ||||||
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Title | Bianthranilate-like analogue bound in the outer site of anthranilate phosphoribosyltransferase (AnPRT; trpD) | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Magnesium binding / phosphoribosylpyrophosphate / PRPP / inhibitor complex / bi-anthranilate-like 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: 1.6683 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 | 4gkm.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gkm.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 4gkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gkm_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4gkm_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4gkm_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 4gkm_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/4gkm ftp://data.pdbj.org/pub/pdb/validation_reports/gk/4gkm | HTTPS FTP |
-Related structure data
Related structure data | 4giuC 4ij1C 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
-Protein / Sugars , 2 types, 4 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 #2: Sugar | |
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-Non-polymers , 5 types, 501 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: 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: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M imidazole.malate, 13% PEG-4000, 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: 0.991841 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2011 |
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991841 Å / Relative weight: 1 |
Reflection | Resolution: 1.667→111.44 Å / Num. all: 81124 / Num. obs: 81071 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.667→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: chain A of PDB ENTRY 3QR9 Resolution: 1.6683→56.474 Å / SU B: 21.32 / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 27.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.457 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6683→56.474 Å
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Refine LS restraints |
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LS refinement shell |
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