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- PDB-2tps: THIAMIN PHOSPHATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 2tps
TitleTHIAMIN PHOSPHATE SYNTHASE
ComponentsPROTEIN (THIAMIN PHOSPHATE SYNTHASE)
KeywordsTHIAMIN BIOSYNTHESIS / TIM BARREL
Function / homology
Function and homology information


thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Thiamine phosphate synthase / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / THIAMIN PHOSPHATE / Thiamine-phosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsChiu, H.-J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E.
CitationJournal: 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
DepositionMar 9, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (THIAMIN PHOSPHATE SYNTHASE)
B: PROTEIN (THIAMIN PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7168
Polymers48,6252
Non-polymers1,0916
Water7,999444
1
A: PROTEIN (THIAMIN PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8584
Polymers24,3131
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (THIAMIN PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8584
Polymers24,3131
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.830, 76.830, 140.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999757, -0.021512, 0.004717), (0.020668, -0.99045, -0.136313), (0.007605, -0.136182, 0.990655)
Vector: 77.664, 78.6027, 4.6615)

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Components

#1: Protein PROTEIN (THIAMIN PHOSPHATE SYNTHASE)


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 ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O4PS
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 35 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMTris-HCl1drop
32 mMdithiothreitol1drop
475 mMTris-HCl1reservoir
575 mM1reservoirMgCl2
624-26 %(v/v)PEG40001reservoir
72 mMbeta-mercaptoethanol1reservoir
85 mMbeta-octylglucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9795,0.9792,0.9677
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97921
30.96771
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 4747 5 %5% OF THIN SHELLS
all0.1807 94169 --
obs0.1792 -81.6 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum non hydrogen: 3962.6
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 64 444 3922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d2.344
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg23.886
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg2.56

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