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- PDB-2hm9: Solution structure of dihydrofolate reductase complexed with trim... -

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Basic information

Entry
Database: PDB / ID: 2hm9
TitleSolution structure of dihydrofolate reductase complexed with trimethoprim, 33 structures
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Oxidoreductase / DHFR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TRR / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Birdsall, B.
CitationJournal: Biochemistry / Year: 2011
Title: NMR structures of apo L.casei dihydrofolate reductase and its complexes with trimethoprim and NADPH. Contributions to positive cooperative binding from ligand-induced refolding, conformational ...Title: NMR structures of apo L.casei dihydrofolate reductase and its complexes with trimethoprim and NADPH. Contributions to positive cooperative binding from ligand-induced refolding, conformational changes and interligand hydrophobic interactions
Authors: Feeney, J. / Birdsall, B. / Kovalevskaya, N.V. / Smurnyy, Y.D. / Navarro-Peran, E.M. / Polshakov, V.I.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6232
Polymers18,3321
Non-polymers2911
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / 33all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: folA, dhfR / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): Nf1 / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-TRR / 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM


Mass: 291.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N4O3 / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1222D NOESY
1332D NOESY
1422D 15N rejected NOESY
151J-MODULATED N15,1H-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM DHFR-15N/TMP, 50mM phosphate buffer, 5% DMPC/DHPC (3:1), 90% H2O, 10% D2O90% H2O/10% D2O
21mM DHFR-15N/TMP, 50mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
31mM DHFR-15N/TMP, 50mM phosphate buffer, 100% D2O100% D2O
Sample conditionsIonic strength: 100mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYVarianUNITY6002
Varian UNITYPLUSVarianUNITYPLUS6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inccollection
NMRPipe1998-2001Delaglioprocessing
Sparky3.8UCSFdata analysis
XPLOR-NIH3.11Clorerefinement
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Annealing from 1000K down to 0K with 25K step, 10ps trajectory on each step
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 33 / Conformers submitted total number: 33

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