[English] 日本語
Yorodumi- PDB-4zok: Methylsulfonyl-containing inhibitor bound in the substrate captur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zok | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Methylsulfonyl-containing inhibitor bound in the substrate capture site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD) | |||||||||
Components | Anthranilate phosphoribosyltransferase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / complex / Lobenzarit-like analogue / TB Structural Genomics Consortium / TBSGC / phosphoribosyltransferase / magnesium binding / phosphoribosylpyrophosphate / PRPP / 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 H37Ra (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Evans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | |||||||||
Funding support | New Zealand, 2items
| |||||||||
Citation | Journal: To be Published Title: Inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD). Authors: Evans, G.L. / Baker, E.N. / Lott, J.S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zok.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zok.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/4zok ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zok | HTTPS FTP |
---|
-Related structure data
Related structure data | 4zofC 4zojC 3qr9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38948.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria) Strain: ATCC 25177 / H37Ra / Gene: trpD, MRA_2208 / Plasmid: pET23A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pGroESL References: UniProt: A5U4M0, anthranilate phosphoribosyltransferase #2: Chemical | ChemComp-MG / #3: Sugar | #4: Chemical | ChemComp-62L / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % / Description: Flat diamond shape |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M imidazole-malate, 11% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2014 |
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: 2.34→36 Å / Num. obs: 29113 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 4.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3QR9 chain A Resolution: 2.34→35.497 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.25 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→35.497 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|