[English] 日本語
Yorodumi- PDB-4n93: Alternative substrates of Mycobacterium tuberculosis anthranilate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n93 | ||||||
---|---|---|---|---|---|---|---|
Title | Alternative substrates of Mycobacterium tuberculosis anthranilate phosphoribosyl transferase | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor / Magnesium binding Phosphoribosyl pyrophosphate | ||||||
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 / molecular replacement / Resolution: 2.03 Å | ||||||
Authors | Castell, A. / Short, F.L. / Lott, J.S. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis. Authors: Cookson, T.V. / Castell, A. / Bulloch, E.M. / Evans, G.L. / Short, F.L. / Baker, E.N. / Lott, J.S. / Parker, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4n93.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4n93.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 4n93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n93_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4n93_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4n93_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 4n93_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n93 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n93 | HTTPS FTP |
-Related structure data
Related structure data | 4n5vC 4n8qC 4owmC 4ownC 4owoC 4owqC 4owsC 4owuC 4owvC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is the same as asym. |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 38790.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2248, MTCY190.03c, Rv2192c, trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P66992, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase #5: Sugar | |
---|
-Non-polymers , 4 types, 554 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-6M1 / #4: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.13 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole/malate, 7.5% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon double crystal Reflections / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→121.424 Å / Num. all: 58284 / Num. obs: 58284 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.09 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→73.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.1627 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.874 / SU B: 3.431 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1546 / SU Rfree: 0.1464 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / ESU R: 0.155 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.05 Å2 / Biso mean: 23.8943 Å2 / Biso min: 9.42 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→73.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.032→2.085 Å / Total num. of bins used: 20
|