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- PDB-3mel: Crystal Structure of Thiamin pyrophosphokinase family protein fro... -

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Basic information

Entry
Database: PDB / ID: 3mel
TitleCrystal Structure of Thiamin pyrophosphokinase family protein from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR150
ComponentsThiamin pyrophosphokinase family protein
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / THIAMINE DIPHOSPHATE / Thiamine pyrophosphokinase family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 2.788 Å
AuthorsKuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. ...Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / 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 EfR150
Authors: Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Authors: Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 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 1.3Apr 3, 2024Group: 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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 family protein
B: Thiamin pyrophosphokinase family protein
C: Thiamin pyrophosphokinase family protein
D: Thiamin pyrophosphokinase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,81619
Polymers101,5084
Non-polymers1,30815
Water1086
1
A: Thiamin pyrophosphokinase family protein
B: Thiamin pyrophosphokinase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,44411
Polymers50,7542
Non-polymers6909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-64 kcal/mol
Surface area17910 Å2
MethodPISA
2
C: Thiamin pyrophosphokinase family protein
D: Thiamin pyrophosphokinase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3728
Polymers50,7542
Non-polymers6186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-68 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.286, 102.112, 94.277
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdimer,52.62 kD,96%

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Components

#1: Protein
Thiamin pyrophosphokinase family protein


Mass: 25377.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_3117 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q82ZE3
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: MgSO4 - 0.15M, Bis-Tris 0.1M, PEG8K 16%, ATP, MgCl2, thiamine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2010 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.788→50 Å / Num. obs: 56964 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MRSADRickShaw serverphasing
REFMACrefinement
RefinementMethod to determine structure: molecular replacementSAD
Starting model: GtR2

Resolution: 2.788→48.53 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1475 5.09 %
Rwork0.2075 --
obs0.2109 29000 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.874 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 46.98 Å2
Refinement stepCycle: LAST / Resolution: 2.788→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6780 0 73 6 6859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097004
X-RAY DIFFRACTIONf_angle_d1.2689554
X-RAY DIFFRACTIONf_dihedral_angle_d21.5532612
X-RAY DIFFRACTIONf_chiral_restr0.0771051
X-RAY DIFFRACTIONf_plane_restr0.0071253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7883-2.87830.30141360.26772337X-RAY DIFFRACTION94
2.8783-2.98110.39981340.26992496X-RAY DIFFRACTION99
2.9811-3.10050.31621540.25272491X-RAY DIFFRACTION99
3.1005-3.24160.29091080.22812520X-RAY DIFFRACTION100
3.2416-3.41240.26451330.21252509X-RAY DIFFRACTION100
3.4124-3.62620.29711270.21532526X-RAY DIFFRACTION100
3.6262-3.9060.25381260.1972520X-RAY DIFFRACTION100
3.906-4.29890.22861390.17712480X-RAY DIFFRACTION100
4.2989-4.92040.20951200.14912552X-RAY DIFFRACTION100
4.9204-6.19720.29471550.19012521X-RAY DIFFRACTION100
6.1972-48.53720.24541430.20822573X-RAY DIFFRACTION100

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