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Yorodumi- PDB-4owu: Anthranilate phosphoribosyl transferase from Mycobacterium tuberc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4owu | ||||||
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Title | Anthranilate phosphoribosyl transferase from Mycobacterium tuberculosis in complex with 5-methylanthranilate, PRPP and Magnesium | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor | ||||||
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 / Resolution: 1.89 Å | ||||||
Authors | Castell, A. / Cookson, T.V.M. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4owu.cif.gz | 271.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4owu.ent.gz | 218.9 KB | Display | PDB format |
PDBx/mmJSON format | 4owu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4owu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4owu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4owu_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 4owu_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4owu ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owu | HTTPS FTP |
-Related structure data
Related structure data | 4n5vC 4n8qC 4n93C 4owmC 4ownC 4owoC 4owqC 4owsC 4owvC C: citing same article (ref.) |
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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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Details | biological unit is the same as asym. |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 38848.883 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 #3: Sugar | |
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-Non-polymers , 5 types, 527 molecules
#2: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #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: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: imidazole/malate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→120.801 Å / Num. all: 71474 / Num. obs: 71474 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Rsym value: 0.065 / Net I/av σ(I): 10.238 / Net I/σ(I): 20.6 / Num. measured all: 515254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.89→73.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.555 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.44 Å2 / Biso mean: 21.995 Å2 / Biso min: 11.2 Å2
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Refinement step | Cycle: final / Resolution: 1.89→73.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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