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- PDB-1xoy: Solution structure of At3g04780.1, an Arabidopsis ortholog of the... -

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Basic information

Entry
Database: PDB / ID: 1xoy
TitleSolution structure of At3g04780.1, an Arabidopsis ortholog of the C-terminal domain of human thioredoxin-like protein
Componentshypothetical protein At3g04780.1Hypothesis
KeywordsStructural Genomics / unknown function / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / PSI / CESG
Function / homology
Function and homology information


PITH domain / PITH domain / PITH domain superfamily / PITH domain / PITH domain profile. / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PITH domain-containing protein At3g04780
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSong, J. / Robert, C.T. / Lee, M.S. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein.
Authors: Song, J. / Tyler, R.C. / Wrobel, R.L. / Frederick, R.O. / Vojtek, F.C. / Jeon, W.B. / Lee, M.S. / Markley, J.L.
History
DepositionOct 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein At3g04780.1


Theoretical massNumber of molelcules
Total (without water)17,9181
Polymers17,9181
Non-polymers00
Water0
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 #1lowest energy

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Components

#1: Protein hypothetical protein At3g04780.1 / Hypothesis


Mass: 17918.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SQZ9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D C(CO)NH

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Sample preparation

DetailsContents: 1 mM U-15N,13C At3g04780.1, 50 mM KH2PO4, 10 mM DTT, 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 298.2 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
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
XwinNMR2.6Brukercollection
NMRPipe97.027.12.56Delaglioprocessing
Sparky3.72Goddard T.D., Kneller, D.G.data analysis
CYANA1.06Guntertstructure solution
Xplor-NIH2.9.3Schwieters, et al.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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