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- PDB-2jyb: binary hvDHFR1:folate complex -

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Basic information

Entry
Database: PDB / ID: 2jyb
Titlebinary hvDHFR1:folate complex
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / Halophilic / Folate / NADP / One-carbon metabolism
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / 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
Dihydrofolate reductase HdrA
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsBoroujerdi, A.A.F.B. / Young, J.K.
CitationJournal: Biopolymers / Year: 2009
Title: NMR-derived folate-bound structure of dihydrofolate reductase 1 from the halophile Haloferax volcanii.
Authors: Boroujerdi, A.F. / Young, J.K.
History
DepositionDec 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)17,9841
Polymers17,9841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Dihydrofolate reductase


Mass: 17983.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P15093, dihydrofolate reductase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D (H)CCH-TOCSY
1913D HCC-TOCSY
11013D CCC-TOCSY
11113D 15N-NOESY-HSQC
11213D 13-NOESY-HSQC

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] hvDHFR1, 2 mM folate, 3.5 M sodium chloride, 10 mM TRIS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMhvDHFR1[U-100% 13C; U-100% 15N]1
2 mMfolate1
3.5 Msodium chloride1
10 mMTRIS1
Sample conditionsIonic strength: 3.5 / pH: 8.25 / Pressure: ambient / Temperature: 307 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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