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- PDB-1ig0: Crystal Structure of yeast Thiamin Pyrophosphokinase -

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Basic information

Entry
Database: PDB / ID: 1ig0
TitleCrystal Structure of yeast Thiamin Pyrophosphokinase
ComponentsThiamin pyrophosphokinase
KeywordsTRANSFERASE / Protein-substrate complex / compound active site / alpha-beta-alpha / beta sandwich
Function / homology
Function and homology information


Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / cytoplasm
Similarity search - Function
Thiamin pyrophosphokinase, eukaryotic / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, thiamin-binding domain superfamily / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily ...Thiamin pyrophosphokinase, eukaryotic / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, thiamin-binding domain superfamily / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-VIB / Thiamine pyrophosphokinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsBaker, L.-J. / Dorocke, J.A. / Harris, R.A. / Timm, D.E.
CitationJournal: Structure / Year: 2001
Title: The crystal structure of yeast thiamin pyrophosphokinase.
Authors: Baker, L.J. / Dorocke, J.A. / Harris, R.A. / Timm, D.E.
History
DepositionApr 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Thiamin pyrophosphokinase
B: Thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8494
Polymers73,3182
Non-polymers5312
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-18 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.313, 130.839, 44.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Thiamin pyrophosphokinase


Mass: 36659.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THI80 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35202, thiamine diphosphokinase
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEGMME 2000, ammonium sulfate, sodium acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.7 mg/mlprotein1drop
266.7 mMthiamin solution1drop
319 %PEG20001reservoir
4100 mMammonium sulfate1reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 27, 1999 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.46 Å / Num. all: 61167 / Num. obs: 60988 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.301 / % possible all: 80.3
Reflection
*PLUS
Num. measured all: 303494
Reflection shell
*PLUS
% possible obs: 74.1 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.46 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1842627.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3004 4.9 %RANDOM
Rwork0.217 ---
obs0.217 60988 94 %-
all-64760 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.33 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2--1.26 Å20 Å2
3---1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 36 670 5830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 418 4.9 %
Rwork0.301 8118 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4THI
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.301

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