+Open data
-Basic information
Entry | Database: PDB / ID: 2tps | ||||||
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Title | THIAMIN PHOSPHATE SYNTHASE | ||||||
Components | PROTEIN (THIAMIN PHOSPHATE SYNTHASE) | ||||||
Keywords | 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 / MAD / Resolution: 1.25 Å | ||||||
Authors | Chiu, H.-J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution. Authors: Chiu, H.J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tps.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tps.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 2tps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tps_validation.pdf.gz | 945.4 KB | Display | wwPDB validaton report |
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Full document | 2tps_full_validation.pdf.gz | 953.2 KB | Display | |
Data in XML | 2tps_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2tps_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/2tps ftp://data.pdbj.org/pub/pdb/validation_reports/tp/2tps | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999757, -0.021512, 0.004717), Vector: |
-Components
#1: Protein | Mass: 24312.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: DE3 / References: UniProt: P39594, thiamine phosphate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE FOLLOWING RESIDUES ARE NOT PART OF THE SWISS-PROT DATABASE ENTRY FOR CHAINS A & B: HIS9, HIS10, ...THE FOLLOWING RESIDUES ARE NOT PART OF THE SWISS-PROT DATABASE ENTRY FOR CHAINS A & B: HIS9, HIS10, GLY11, ILE12, ARG13. | |
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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: 2.05 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: 75 MM TRIS-HCL, PH 7.5 21-22% PEG4000 75 MM MGCL2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.9795,0.9792,0.9677 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.25→30 Å / Num. obs: 94169 / % possible obs: 81.6 % / Redundancy: 5.1 % / Rsym value: 0.062 / Net I/σ(I): 6.8 | ||||||||||||
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.219 / % possible all: 48.5 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.062 | ||||||||||||
Reflection shell | *PLUS % possible obs: 48.5 % / Rmerge(I) obs: 0.219 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.25→8 Å / Num. parameters: 18915 / Num. restraintsaints: 18840 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE STRUCTURE WAS REFINED WITH X-PLOR AND FOLLOWED BY SHELXL
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Refine analyze | Num. disordered residues: 9 / Occupancy sum non hydrogen: 3962.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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