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- PDB-2jmu: NMR structure of the mouse thiamine triphosphatase -

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Basic information

Entry
Database: PDB / ID: 2jmu
TitleNMR structure of the mouse thiamine triphosphatase
ComponentsThiamine-triphosphatase
KeywordsHYDROLASE / thiamine triphosphatase / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


thiamine-triphosphatase / thiamine diphosphate metabolic process / thiamine triphosphate phosphatase activity / Vitamin B1 (thiamin) metabolism / thiamine metabolic process / thiamine diphosphate biosynthetic process / dephosphorylation / magnesium ion binding / cytosol
Similarity search - Function
Thiamine triphosphatase, eukaryotes / Thiamine-triphosphatase / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Thiamine-triphosphatase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing,distance geometry
AuthorsSong, J. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase.
Authors: Song, J. / Bettendorff, L. / Tonelli, M. / Markley, J.L.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine-triphosphatase


Theoretical massNumber of molelcules
Total (without water)24,2431
Polymers24,2431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thiamine-triphosphatase / ThTPase


Mass: 24243.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Thtpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) pLysS / References: UniProt: Q8JZL3, thiamine-triphosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
1411H,13C-HSQC
151CBCA(CO)NH
161C(CO)NH
171HCCHTOCSY
181HBACONH
19113C-EDITED 1H,1H-NOESY
110115N-EDITED 1H,1H-NOESY
111113C-EDITED AROMATIC 1H,1H-NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] ThTPase_MOUSE, 10 mM MOPS, 100 mM NaCl, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMThTPase_MOUSE[U-100% 13C; U-100% 15N]1
10 mMMOPS1
100 mMNaCl1
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3Schwieters, Kuszewski, Tjandra and Clorerefinement
XwinNMR3.5Brukercollection
NMRPipe97.027.12.56Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddard and Knellerdata analysis
GARANT2.1Bartels, Guntert, Billeter and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructural calculation
RefinementMethod: torsion angle dynamics,simulated annealing,distance geometry
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 4699 NOE RESTRAINTS (1639 INTRA, 921 SEQUENTIAL, 757 MEDIUM AND 1382 LONG RANGE), 176 HBOND RESTRAINTS, AND 289 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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