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- PDB-3ihk: Crystal Structure of thiamin pyrophosphokinase from S.mutans, Nor... -

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Basic information

Entry
Database: PDB / ID: 3ihk
TitleCrystal Structure of thiamin pyrophosphokinase from S.mutans, Northeast Structural Genomics Consortium Target SmR83
Componentsthiamin pyrophosphokinase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SmR83 / Q8DVV9 / thiamin pyrophosphokinase
Function / homology
Function and homology information


thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / THIAMINE DIPHOSPHATE / TPK_B1_binding domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phenix / Resolution: 3 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Vorobiev, S. / Mao, M. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Vorobiev, S. / Mao, M. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target SmR83
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Vorobiev, S. / Mao, M. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / ...Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Vorobiev, S. / Mao, M. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thiamin pyrophosphokinase
B: thiamin pyrophosphokinase
C: thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,21928
Polymers75,2783
Non-polymers2,94125
Water181
1
A: thiamin pyrophosphokinase
hetero molecules

A: thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27320
Polymers50,1852
Non-polymers2,08818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7940 Å2
ΔGint-142 kcal/mol
Surface area17150 Å2
MethodPISA
2
B: thiamin pyrophosphokinase
C: thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08318
Polymers50,1852
Non-polymers1,89816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-128 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.157, 105.157, 121.383
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsdimer,53.26 kD,99.0%

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Components

#1: Protein thiamin pyrophosphokinase


Mass: 25092.607 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_353 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DVV9
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M LiCl, 0.1M Bis-Tris, 18% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97884 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 59849 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: Phenix / Resolution: 3→20 Å / σ(F): 3997 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.243 1301 4.3 %
Rwork0.203 --
obs-25262 84.3 %
Solvent computationBsol: 18.982 Å2
Displacement parametersBiso mean: 41.659 Å2
Baniso -1Baniso -2Baniso -3
1-1.728 Å20 Å20 Å2
2--1.728 Å20 Å2
3----3.456 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4943 0 164 1 5108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d2.082
X-RAY DIFFRACTIONc_mcbond_it1.2571.5
X-RAY DIFFRACTIONc_scbond_it1.9892
X-RAY DIFFRACTIONc_mcangle_it2.1682
X-RAY DIFFRACTIONc_scangle_it3.062.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2ppi.parppi.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5tpp.partpp.top

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