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Yorodumi- PDB-4n5v: Alternative substrates of Mycobacterium tuberculosis anthranilate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n5v | ||||||
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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 / Resolution: 1.9 Å | ||||||
Authors | Castell, A. / Cookson, T.V.M. / Parker, E.J. / Baker, E.N. / 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 | 4n5v.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n5v.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n5v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4n5v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4n5v_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 4n5v_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5v ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5v | HTTPS FTP |
-Related structure data
Related structure data | 4n8qC 4n93C 4owmC 4ownC 4owoC 4owqC 4owsC 4owuC 4owvC 3qr9S S: Starting model for refinement 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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-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) / Strain: H37Rv / 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 #2: Sugar | |
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-Non-polymers , 4 types, 524 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-FA0 / #5: Chemical | #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: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 296 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 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 |
Radiation | Monochromator: Silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→121.06 Å / Num. obs: 71154 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.108 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 2 / Num. unique all: 69643 / Rsym value: 1.093 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QR9 Resolution: 1.9→73.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.026 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.619 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→73.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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