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Yorodumi- PDB-3t55: Crystal structure of Mycobacterium tuberculosis Indole Glycerol P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t55 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with Phenoxymethyl Benzoic Acid (PMBA) | ||||||
Components | Indole-3-glycerol phosphate synthase | ||||||
Keywords | TRANSFERASE / Indole-3-glycerol Phosphate Synthase (IGPS) / Tryptophan biosynthesis / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information 5-phosphoribose 1-diphosphate metabolic process / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å | ||||||
Authors | Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Structural Insights and Inhibition of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS): an Essential Enzyme for Tryptophan Biosynthesis Authors: Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t55.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t55.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 3t55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t55 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t55 | HTTPS FTP |
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-Related structure data
Related structure data | 3t40C 3t44C 3t78C 1igsS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 28053.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1646, MTCY01B2.03, Rv1611, trpC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A632, UniProt: P9WFX7*PLUS, indole-3-glycerol-phosphate synthase |
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#2: Chemical | ChemComp-4RG / |
#3: Chemical | ChemComp-MLI / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97711 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97711 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.06→50 Å / Num. all: 13524 / Num. obs: 13524 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Χ2: 3.486 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 Starting model: PDB entry 1IGS Resolution: 2.06→40.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2423 / WRfactor Rwork: 0.1803 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8197 / SU B: 5.174 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2592 / SU Rfree: 0.2105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.21 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.41 Å2 / Biso mean: 24.0498 Å2 / Biso min: 9.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→40.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.118 Å / Total num. of bins used: 20
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