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Yorodumi- PDB-3twp: Crystal structure of M. tuberculosis TrpD in complex with an inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3twp | ||||||
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Title | Crystal structure of M. tuberculosis TrpD in complex with an inhibitor | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Transferase / Magnesium binding Phosphoribosyl pyrophosphate / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | ||||||
Authors | Castell, A. / Short, F.L. / Lott, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition. Authors: Castell, A. / Short, F.L. / Evans, G.L. / Cookson, T.V. / Bulloch, E.M. / Joseph, D.D. / Lee, C.E. / Parker, E.J. / Baker, E.N. / 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 | 3twp.cif.gz | 288 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3twp.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 3twp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3twp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3twp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3twp_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 3twp_validation.cif.gz | 91.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/3twp ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3twp | HTTPS FTP |
-Related structure data
Related structure data | 3qqsC 3qr9C 3qs8C 3r6cC 3r88C 3uu1C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 38717.688 Da / Num. of mol.: 4 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 #2: Sugar | ChemComp-PRP / |
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-Non-polymers , 4 types, 1214 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SAL / #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: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M cacodylate, 10% PEG-6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→111.263 Å / Num. all: 118766 / Num. obs: 118766 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.044 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→81.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / 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: 20.655 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→81.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.878 Å / Total num. of bins used: 20
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