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- PDB-5tcf: Crystal structure of tryptophan synthase from M. tuberculosis - l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tcf | ||||||||||||
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Title | Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form | ||||||||||||
![]() | (Tryptophan synthase ...) x 2 | ||||||||||||
![]() | LYASE / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Michalska, K. / Maltseva, N. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase. Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / ...Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / Fisher, S.L. / Joachimiak, A. / Schreiber, S.L. / Hung, D.T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 959.5 KB | Display | ![]() |
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PDB format | ![]() | 794.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5tcgC ![]() 5tchC ![]() 5tciC ![]() 5tcjC ![]() 1kfjS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Tryptophan synthase ... , 2 types, 8 molecules AGECBHFD
#1: Protein | Mass: 28579.449 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Plasmid: pMCSG81, pMCSG81-pRSF Details (production host): pMCSG81 coexpresses TrpA with TrpB, pMCSG81-pRSF provides additional copy of TrpA Production host: ![]() ![]() #2: Protein | Mass: 43562.711 Da / Num. of mol.: 4 / Fragment: UNP 13-422 Source method: isolated from a genetically manipulated source Details: Lys101 is attached to PLP Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: pMCSG81 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 493 molecules ![](data/chem/img/MLI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MLI / #4: Chemical | ChemComp-FMT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 8% tacsimate pH 8.0, 20% PEG3350, 100 mM KCl, cryo 17% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2015 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 128446 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.36 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.03 / CC1/2: 0.703 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KFJ Resolution: 2.46→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.9 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.205 / 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 mean: 42.53 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→30 Å
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Refine LS restraints |
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