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- PDB-3k94: Crystal Structure of Thiamin pyrophosphokinase from Geobacillus t... -

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Basic information

Entry
Database: PDB / ID: 3k94
TitleCrystal Structure of Thiamin pyrophosphokinase from Geobacillus thermodenitrificans, Northeast Structural Genomics Consortium Target GtR2
ComponentsThiamin pyrophosphokinaseThiamine diphosphokinase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / GtR2 / Kinase
Function / homology
Function and homology information


thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding
Similarity search - Function
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 superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold ...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 superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiamine diphosphokinase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.101 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. ...Kuzin, A. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / 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 GtR2
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 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


Theoretical massNumber of molelcules
Total (without water)50,9702
Polymers50,9702
Non-polymers00
Water4,504250
1
A: Thiamin pyrophosphokinase

B: Thiamin pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)50,9702
Polymers50,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2700 Å2
ΔGint-15 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.422, 73.652, 82.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthor provided the following information on possible biological assembly: dimer,55.92 kD, 87.2%; heptamer, 129.5 kD, 8.2%

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Components

#1: Protein Thiamin pyrophosphokinase / Thiamine diphosphokinase


Mass: 25484.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: GTNG_1032 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A4IM54
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAt least two cysteine, residues 26 and 185 of chain A and B, have some electron density beyond the ...At least two cysteine, residues 26 and 185 of chain A and B, have some electron density beyond the oxygen atom in the side chain.

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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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 4.2
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Na-citrate, 0.1M (NH4)2HPO4, 20% PEG 4000, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 3, 2009 / Details: Si(111)
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 46746 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.85 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.101→26.353 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1264 5.08 %
Rwork0.1769 --
obs0.1802 24867 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.681 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 35.767 Å2
Refinement stepCycle: LAST / Resolution: 2.101→26.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 0 250 3642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073470
X-RAY DIFFRACTIONf_angle_d1.0774709
X-RAY DIFFRACTIONf_dihedral_angle_d16.4071271
X-RAY DIFFRACTIONf_chiral_restr0.065532
X-RAY DIFFRACTIONf_plane_restr0.005605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1011-2.18520.2721410.19222521X-RAY DIFFRACTION98
2.1852-2.28450.27181270.1832613X-RAY DIFFRACTION100
2.2845-2.40490.26891460.17542561X-RAY DIFFRACTION100
2.4049-2.55550.23721390.17912618X-RAY DIFFRACTION100
2.5555-2.75260.28191300.18152620X-RAY DIFFRACTION100
2.7526-3.02920.2691670.18452581X-RAY DIFFRACTION100
3.0292-3.46670.23571350.18172657X-RAY DIFFRACTION100
3.4667-4.36450.21821400.15132666X-RAY DIFFRACTION100
4.3645-26.35550.20811390.1682766X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.6719 Å / Origin y: 36.3177 Å / Origin z: 35.969 Å
111213212223313233
T0.1783 Å2-0.0061 Å2-0.0044 Å2-0.141 Å20.0153 Å2--0.1437 Å2
L0.4817 °20.0857 °20.0011 °2-0.0751 °20.0024 °2--0.0847 °2
S-0.0258 Å °0.0371 Å °0.0745 Å °0.0071 Å °0.0124 Å °0.0105 Å °-0.024 Å °0.0037 Å °0.0123 Å °
Refinement TLS groupSelection details: all

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