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- PDB-1ig3: Mouse Thiamin Pyrophosphokinase Complexed with Thiamin -

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Basic information

Entry
Database: PDB / ID: 1ig3
TitleMouse Thiamin Pyrophosphokinase Complexed with Thiamin
Componentsthiamin pyrophosphokinase
KeywordsTRANSFERASE / beta barrel / alpha/beta/alpha sandwich
Function / homology
Function and homology information


Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / identical protein binding / cytosol
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 / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain ...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 / 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 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTimm, D.E. / Liu, J. / Baker, L.-J. / Harris, R.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of thiamin pyrophosphokinase.
Authors: Timm, D.E. / Liu, J. / Baker, L.J. / Harris, R.A.
History
DepositionApr 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_ref_seq_dif / 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_ref_seq_dif.details / _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)60,41218
Polymers58,5372
Non-polymers1,87616
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-195 kcal/mol
Surface area20870 Å2
MethodPISA
2
A: thiamin pyrophosphokinase
hetero molecules

A: thiamin pyrophosphokinase
hetero molecules

B: thiamin pyrophosphokinase
hetero molecules

B: thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,82536
Polymers117,0744
Non-polymers3,75132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area10550 Å2
ΔGint-362 kcal/mol
Surface area44730 Å2
MethodPISA
3
A: thiamin pyrophosphokinase
B: thiamin pyrophosphokinase
hetero molecules

A: thiamin pyrophosphokinase
B: thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,82536
Polymers117,0744
Non-polymers3,75132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area15480 Å2
ΔGint-400 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.8, 89.8, 141.1
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein thiamin pyrophosphokinase


Mass: 29268.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R0M5, thiamine diphosphokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate, PEG 400, HEPES buffer, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
21.8-2.1 Mammonium sulfate1reservoir
30.1 MHEPES1reservoir
42-4 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 18, 2000 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 52465 / Num. obs: 52413 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5106 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 330681
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 2606 random
Rwork0.214 --
all0.214 51682 -
obs0.214 52413 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 106 413 4406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.427
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.43

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