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- PDB-1g67: THIAMIN PHOSPHATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1g67
TitleTHIAMIN PHOSPHATE SYNTHASE
ComponentsTHIAMIN PHOSPHATE SYNTHASE
KeywordsTRANSFERASE / 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
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
2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE / PYROPHOSPHATE 2- / 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE / Thiamine-phosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsPeapus, 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: 1999
Title: Crystal Structure of Thiamin Phosphate Synthase from Bacillus subtilis at 1.25A Resolution
Authors: Chiu, H.-J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E.
#2: 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
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIAMIN PHOSPHATE SYNTHASE
B: THIAMIN PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,13010
Polymers48,0412
Non-polymers1,0898
Water4,738263
1
A: THIAMIN PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5655
Polymers24,0201
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIAMIN PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5655
Polymers24,0201
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.980, 76.980, 140.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THIAMIN PHOSPHATE SYNTHASE


Mass: 24020.348 Da / Num. of mol.: 2 / Mutation: S130A
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH 2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE, 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE AND PYROPHOSPHATE
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

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Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ICP / 2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE / 4-IMINO-5-METHIDYL-2-METHYLPYRIMIDINE


Mass: 121.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7N3
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-TZP / 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE


Mass: 223.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO4PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion with micro seeding / pH: 7.5
Details: 75mM TRIS-HCl, 75 mM MgCl2, 21-22% PEG4000 , pH 7.5, 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
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: 0.921
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 1.4→42.99 Å / Num. obs: 64370 / % possible obs: 77 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.9
Reflection
*PLUS
Num. obs: 65601 / % possible obs: 78.7 %
Reflection shell
*PLUS
% possible obs: 64.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1G4E

1g4e


Resolution: 1.4→42.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 398888.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Maximum Likelihood Function
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3246 5 %RANDOM
Rwork0.216 ---
obs0.216 64370 77 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.53 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.4→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 72 263 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 418 5.1 %
Rwork0.252 7859 -
obs--60.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4C2.PARAMC2.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.252

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