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- PDB-1g4e: THIAMIN PHOSPHATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1g4e
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 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
Thiamine-phosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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
DepositionOct 26, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,5932
Polymers48,5932
Non-polymers00
Water5,783321
1
A: THIAMIN PHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,2971
Polymers24,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIAMIN PHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,2971
Polymers24,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.370, 76.370, 139.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein THIAMIN PHOSPHATE SYNTHASE


Mass: 24296.643 Da / Num. of mol.: 2 / Mutation: S130A
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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 / pH: 7.5
Details: 75mM TRIS-HCl, 75mM MgCl2, 21-22% PEG4000 , pH 7.5, 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, 2000
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 1.6→26.51 Å / Num. obs: 52317 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.2
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.5

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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 2TPS

2tps


Resolution: 1.6→26.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 776136.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2646 5.1 %RANDOM
Rwork0.21 ---
obs0.21 52317 94.9 %-
all-54963 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.87 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 0 321 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 411 5.4 %
Rwork0.211 7271 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.5 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_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
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: 0.242 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.211

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