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- PDB-1xne: Solution Structure of Pyrococcus furiosus Protein PF0470: The Nor... -

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Basic information

Entry
Database: PDB / ID: 1xne
TitleSolution Structure of Pyrococcus furiosus Protein PF0470: The Northeast Structural Genomics Consortium Target PfR14
Componentshypothetical protein PF0469
KeywordsStructural Genomics / Unknown Function / GFT NMR / Protein Structure Initiative / PSI / NESG / PfR14 / alpha and beta protein / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Uncharacterised conserved protein UCP016134 / Hypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ASCH domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsLiu, G. / Xiao, R. / Parish, D. / Ma, L. / Sukumaran, D. / Acton, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: NMR data collection and analysis protocol for high-throughput protein structure determination.
Authors: Liu, G. / Shen, Y. / Atreya, H.S. / Parish, D. / Shao, Y. / Sukumaran, D.K. / Xiao, R. / Yee, A. / Lemak, A. / Bhattacharya, A. / Acton, T.A. / Arrowsmith, C.H. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PF0469


Theoretical massNumber of molelcules
Total (without water)13,8171
Polymers13,8171
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein hypothetical protein PF0469


Mass: 13817.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3J6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CabCa(CO)NHN
131GFT (4,3)D HabCab(CO)NHN
141GFT (4,3) (H)CCH
151Simultaneous Heteronuclear Resolved -NOESY
NMR detailsText: High throughput structure determination by GFT NMR techniques

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Sample preparation

DetailsContents: 1.02 mM, NMR Buffer 6.5, 5% D2O, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
XEASY1.3.1.3Bartels, C.data analysis
DYANA1.5Guentert, P.structure solution
DYANA1.5Guentert, P.refinement
AutoAssign1.13.2Zimmerman, D.E.data analysis
CYANA1.0.5Guentert, Pdata analysis
AutoStructure2.0.0Huang, Y.J.data analysis
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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