+Open data
-Basic information
Entry | Database: PDB / ID: 1g4t | ||||||
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Title | THIAMIN PHOSPHATE SYNTHASE | ||||||
Components | THIAMIN PHOSPHATE SYNTHASE | ||||||
Keywords | TRANSFERASE / THIAMIN BIOSYNTHESIS / TIM BARREL | ||||||
Function / homology | Function and homology information thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Peapus, D.H. / Chiu, H.-J. / Campobasso, N. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. Authors: Peapus, D.H. / Chiu, H.J. / Campobasso, N. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. #1: Journal: Biochemistry / Year: 2001 Title: Mechanistic Studies on Thiamin Phosphate Synthase: Evidence for a Dissociative Mechanism Authors: Reddick, J.J. / Nicewonger, R. / Begley, T.P. #2: Journal: Biochemistry / Year: 1999 Title: Crystal Structure of Thiamine Phosphate Synthase from Bacillus subtilis at 1.25A Resolution Authors: Chiu, H.-J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. #3: Journal: J.BACTERIOL. / Year: 1997 Title: CHARACTERIZATION OF THE BACILLUS SUBTILIS THIC OPERON INVOLVED IN THIAMINE BIOSYNTHESIS Authors: ZHANG, Y. / TAYLOR, S.V. / CHIU, H.-J. / BEGLEY, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g4t.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g4t.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g4t ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g4t | HTTPS FTP |
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-Related structure data
Related structure data | 1g4eSC 1g4pC 1g4sC 1g67C 1g69C 1g6cC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24312.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH TRIFLUORO-THIAMIN PHOSPHATE / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: THIC / Plasmid: PYZC6927 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 WITH PREP4 / References: UniProt: P39594, thiamine phosphate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.01 Å3/Da / Density % sol: 38.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K Method: protein:ligand cocrystallization, hanging drop vapor diffusion with micro seeding pH: 7.5 Details: 75mM TRIS-HCl, 75 mM MgCl2, 21-22% PEG4000 , pH 7.5, protein:ligand cocrystallization, hanging drop vapor diffusion with micro seeding, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: Chiu, H.-J., (1999) Biochemistry, 38, 6460. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.921 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998 |
Radiation | Monochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.921 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.94 Å / Num. obs: 59361 / % possible obs: 96.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.3 |
Reflection | *PLUS Num. obs: 60821 / % possible obs: 98.6 % |
Reflection shell | *PLUS % possible obs: 92.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1G4E Resolution: 1.55→42.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 778487.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Maximum Likelihood Function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.72 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→42.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.233 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.303 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.252 |