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- PDB-2f17: Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithi... -

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Basic information

Entry
Database: PDB / ID: 2f17
TitleMouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom
ComponentsThiamin pyrophosphokinase 1
KeywordsTRANSFERASE / BETA BARREL / ALPHA/BETA/ALPHA SANDWICH / pyrophosphokinase / AMP
Function / homology
Function and homology information


Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / 8-oxo-dGDP phosphatase activity / kinase activity / phosphorylation / ATP binding ...Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / 8-oxo-dGDP phosphatase activity / kinase activity / phosphorylation / 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 pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / 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 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
ADENOSINE MONOPHOSPHATE / Chem-PYI / Thiamin pyrophosphokinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, J.Y. / Timm, D.E. / Hurley, T.D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Pyrithiamine as a substrate for thiamine pyrophosphokinase
Authors: Liu, J.Y. / Timm, D.E. / Hurley, T.D.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,58614
Polymers58,5372
Non-polymers2,04912
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-134 kcal/mol
Surface area20180 Å2
MethodPISA
2
A: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules

A: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,17228
Polymers117,0744
Non-polymers4,09824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area16680 Å2
ΔGint-276 kcal/mol
Surface area38300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.363, 89.363, 141.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe dimer in the asymmetric unit is thought to be the biological unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiamin pyrophosphokinase 1 / Thiamine pyrophosphokinase 1 / mTPK1


Mass: 29268.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpk1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9R0M5, thiamine diphosphokinase

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Non-polymers , 6 types, 144 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PYI / 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM / PYRITHIAMIN PYROPHOSPHATE


Mass: 419.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N4O7P2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: Crystallization experiments were set up by incubating mouse TPK with pyrithiamin and MgATP prior to adding the equilibrium mixture of enzyme, substrate and products to the previously ...Details: Crystallization experiments were set up by incubating mouse TPK with pyrithiamin and MgATP prior to adding the equilibrium mixture of enzyme, substrate and products to the previously determined crystallization conditions. , pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23271 / Num. obs: 21991 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 3.98 % / Biso Wilson estimate: 62.382 Å2 / Rsym value: 0.117 / Net I/σ(I): 8.94
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.12 / Num. unique all: 2271 / Rsym value: 0.614 / % possible all: 96.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IG3

1ig3


Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1085 -Random
Rwork0.237 ---
all0.26 23271 --
obs0.24 21991 94.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 124 132 4153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.318
X-RAY DIFFRACTIONc_dihedral_angle_d24.6627
X-RAY DIFFRACTIONc_improper_angle_d0.9793
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree error: 1.53
RfactorNum. reflection% reflection
Rfree0.362 929 -
Rwork0.347 --
obs-977 79.38 %

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