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Yorodumi- PDB-4fb7: The apo form of idole-3-glycerol phosphate synthase (TrpC) form M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fb7 | ||||||
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Title | The apo form of idole-3-glycerol phosphate synthase (TrpC) form Mycobacterium tuberculosis | ||||||
Components | Indole-3-glycerol phosphate synthase | ||||||
Keywords | LYASE / Structural Genomics / PSI-Biology / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / Midwest Center for Structural Genomics / MCSG / TIM barrel | ||||||
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 / SAD / Resolution: 1.3 Å | ||||||
Authors | Michalska, K. / Chhor, G. / Jedrzejczak, R. / Terwilliger, T.C. / Rubin, E.J. / Guinn, K. / Baker, D. / Ioerger, T.R. / Sacchettini, J.C. / Joachimiak, A. ...Michalska, K. / Chhor, G. / Jedrzejczak, R. / Terwilliger, T.C. / Rubin, E.J. / Guinn, K. / Baker, D. / Ioerger, T.R. / Sacchettini, J.C. / Joachimiak, A. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The apo form of idole-3-glycerol phosphate synthase (TrpC) form Mycobacterium tuberculosis Authors: Michalska, K. / Chhor, G. / Jedrzejczak, R. / Terwilliger, T.C. / Rubin, E.J. / Guinn, K. / Baker, D. / Ioerger, T.R. / Sacchettini, J.C. / Joachimiak, A. / Structures of Mtb Proteins ...Authors: Michalska, K. / Chhor, G. / Jedrzejczak, R. / Terwilliger, T.C. / Rubin, E.J. / Guinn, K. / Baker, D. / Ioerger, T.R. / Sacchettini, J.C. / Joachimiak, A. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fb7.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fb7.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fb7 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fb7 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28606.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1646, MTCY01B2.03, Rv1611, trpC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic References: UniProt: P0A632, UniProt: P9WFX7*PLUS, indole-3-glycerol-phosphate synthase |
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#2: Chemical | ChemComp-BTB / |
#3: 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: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris/HCl, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→50 Å / Num. all: 67985 / Num. obs: 65545 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.12 / Χ2: 1.721 / Net I/σ(I): 21.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→47.26 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 1.276 / SU ML: 0.024 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 88.94 Å2 / Biso mean: 15.3991 Å2 / Biso min: 5.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→47.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.295→1.329 Å / Total num. of bins used: 20
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