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- PDB-1pjz: Solution structure of thiopurine methyltransferase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 1pjz
TitleSolution structure of thiopurine methyltransferase from Pseudomonas syringae
ComponentsThiopurine S-methyltransferaseThiopurine methyltransferase
KeywordsTRANSFERASE / methyltransferase / polymorphism / S-adenosylmethionine / drug metabolism
Function / homology
Function and homology information


thiopurine S-methyltransferase / thiopurine S-methyltransferase activity / response to tellurium ion / response to metal ion / methylation / cytoplasm
Similarity search - Function
Thiopurine S-methyltransferase, Se/Te detoxification / Thiopurine S-methyltransferase / Thiopurine S-methyltransferase (TPMT) / TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiopurine S-methyltransferase
Similarity search - Component
Biological speciesPseudomonas syringae pv. pisi (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsScheuermann, T.H. / Lolis, E. / Hodsdon, M.E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Tertiary structure of thiopurine methyltransferase from Pseudomonas syringae, a bacterial orthologue of a polymorphic, drug-metabolizing enzyme
Authors: Scheuermann, T.H. / Lolis, E. / Hodsdon, M.E.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 999SEQUENCE 17 N-terminal residues were deleted from the sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiopurine S-methyltransferase


Theoretical massNumber of molelcules
Total (without water)22,5901
Polymers22,5901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1

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Components

#1: Protein Thiopurine S-methyltransferase / Thiopurine methyltransferase / Thiopurine methyltransferase / Tellurite-resistance determinant / TEL-R determinant


Mass: 22590.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. pisi (bacteria)
Species: Pseudomonas syringae / Strain: pv. pisi / Gene: TPM / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)BL21 / References: UniProt: O86262, thiopurine S-methyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
141HNHA

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Sample preparation

DetailsContents: 20 mM Potassium Phosphate, 150 mM NaCl, 0.05% NaN3, 1 uM lupeptin, 1 uM pepstatin, 1 uM PMSF, 1.5 mM protein, uniform (random) labeling with 13C, 15N at known labeling
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 150 mM NaCL / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varina, Inc.collection
NMRDraw2.1Delaglio, et al.data analysis
NMRPipeDelaglio, et al.processing
Sparky3.98Goddard, Knellerdata analysis
NMRView5.0.4Johnsondata analysis
CYANA1.05Guentertstructure solution
TALOSCornilescu, et al.data analysis
CYANA1.05Guentertrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: 5000 MD steps at high temp, 35000 steps (cooling), 10000 conjugate gradient minimzation steps
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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