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- PDB-2gmg: Solution NMR Structure of protein PF0610 from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 2gmg
TitleSolution NMR Structure of protein PF0610 from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfG3
Componentshypothetical protein Pf0610
KeywordsDNA BINDING PROTEIN / winged-helix like protein with metal binding site / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTranscriptional regulator containing an HTH domain fused to a Zn-ribbon, predicted / : / : / PF0610-like, N-terminal / PF0610 rubredoxin-like zinc beta-ribbon domain / Winged helix DNA-binding domain superfamily / Transcriptional regulator
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / simulated annealing using torsion angle dynamics
AuthorsWang, X. / Lee, H.S. / Adams, M.W. / Northeast Structural Genomics Consortium (NESG) / Montelione, G.T. / Prestegard, J.H.
CitationJournal: Biochemistry / Year: 2007
Title: PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus.
Authors: Wang, X. / Lee, H.S. / Sugar, F.J. / Jenney, F.E. / Adams, M.W. / Prestegard, J.H.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Pf0610


Theoretical massNumber of molelcules
Total (without water)12,1681
Polymers12,1681
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)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein hypothetical protein Pf0610


Mass: 12168.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: AE010183 / Plasmid: pET-24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U362

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HN(CA)CB
141CBCACONNH
151(H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.5mM Pf0610 U-15N, 13C, 20mM Tris, 150mM NaCl, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.15M / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.15Guntert, P.structure solution
XPLOR-NIH2.14Schwieters, C.D. et al.refinement
RefinementMethod: simulated annealing using torsion angle dynamics / Software ordinal: 1
Details: The structure was refined with 923 NOE-derived distance restraints, 109 back bone dihedral angle restraints and 208 residual dipolar coupling constants
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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