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- PDB-2ith: NMR Structure of Haloferax volcanii DHFR -

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Basic information

Entry
Database: PDB / ID: 2ith
TitleNMR Structure of Haloferax volcanii DHFR
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase / DHFR / Halophilic Archaea
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
AuthorsBinbuga, B.
Citation
Journal: Protein Sci. / Year: 2007
Title: Structure in an extreme environment: NMR at high salt.
Authors: Binbuga, B. / Boroujerdi, A.F. / Young, J.K.
#1: Journal: J.Biomol.Nmr / Year: 2005
Title: 1H, 13C and 15N backbone and side chain resonance assignments of Haloferax volcanii DHFR1.
Authors: Binbuga, B. / Young, J.K.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence Authors state that the original DNA sequence is obtained from hvDHFR. In the previous ...sequence Authors state that the original DNA sequence is obtained from hvDHFR. In the previous studies, residue Val37 was replaced by Ile37 in the sequence.

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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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
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 / Plasmid: pET11-d / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta BL21(DE3) pLysS / 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
111HSQC
121HNCA
131HN(CA)CB
141CBCAHN
151HNCO
161HN(CA)CO
171(H)C(C-CO)NH-TOCSY
181H(CC-CO)NH-TOCSY
191(H)CCH-TOCSY
110115N-edited NOESY
111113C-edited NOESY

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Sample preparation

DetailsContents: 2 mM Protein Sample in 3.5M NaCl, 10mM TRIS BUFFER, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 3.5 M NaCl / pH: 7 / 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
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Version: 1.1 / 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 least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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