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- PDB-3lm8: Crystal Structure of Thiamine pyrophosphokinase from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 3lm8
TitleCrystal Structure of Thiamine pyrophosphokinase from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR677
ComponentsThiamine pyrophosphokinase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ATP-binding / Kinase / Nucleotide-binding
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
PHOSPHATE ION / Chem-VIB / Thiamine pyrophosphokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / 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 SR677
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine pyrophosphokinase
B: Thiamine pyrophosphokinase
C: Thiamine pyrophosphokinase
D: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03317
Polymers101,4704
Non-polymers1,56313
Water1,20767
1
A: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7765
Polymers25,3671
Non-polymers4094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8967
Polymers25,3671
Non-polymers5286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7283
Polymers25,3671
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6332
Polymers25,3671
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Thiamine pyrophosphokinase
C: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5048
Polymers50,7352
Non-polymers7696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
B: Thiamine pyrophosphokinase
D: Thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5289
Polymers50,7352
Non-polymers7947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.943, 62.153, 84.161
Angle α, β, γ (deg.)82.89, 82.02, 87.61
Int Tables number1
Space group name H-MP1
Detailsauthors state that the biological unit is a dimer of 49.65 kD at 99.5%

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Components

#1: Protein
Thiamine pyrophosphokinase / TPK / Thiamine diphosphokinase


Mass: 25367.439 Da / Num. of mol.: 4 / Mutation: A203V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU15800, thiN, yloS / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O34664, 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.: 4 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M KH2PO4, 0.1M Na-acetate, 12% PEG-20K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 21, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 57881 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 1.9 / % possible all: 91

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
REFMACrefinement
RefinementMethod to determine structure: MIR
Starting model: 3K94

3k94


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2422 4 %5%
Rwork0.213 ---
obs0.213 49268 82.4 %-
Solvent computationBsol: 25.78 Å2
Displacement parametersBiso mean: 39.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.106 Å25.735 Å20.544 Å2
2--3.391 Å2-4.241 Å2
3----5.498 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 97 67 6941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2THI.PAR
X-RAY DIFFRACTION3CNS_TOPPAR:WATER.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5TPP.PAR

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