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- PDB-1xo8: Solution structure of AT1g01470 from Arabidopsis Thaliana -

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Basic information

Entry
Database: PDB / ID: 1xo8
TitleSolution structure of AT1g01470 from Arabidopsis Thaliana
ComponentsAt1g01470
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / PSI / CESG
Function / homology
Function and homology information


response to desiccation / response to high light intensity / defense response to fungus / response to wounding / cytosol
Similarity search - Function
Immunoglobulin-like - #1820 / Late embryogenesis abundant protein Lea14-like / Late embryogenesis abundant protein, LEA_2 subgroup / Water stress and hypersensitive response domain / Late embryogenesis abundant protein / Water Stress and Hypersensitive response / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable desiccation-related protein LEA14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle, cartesian coordinate dynamics; water refinement
AuthorsSingh, S. / Cornilescu, C.C. / Tyler, R.C. / Cornilescu, G. / Tonelli, M. / Lee, M.S. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein
Authors: Singh, S. / Cornilescu, C.C. / Tyler, R.C. / Cornilescu, G. / Tonelli, M. / Lee, M.S. / Markley, J.L.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: At1g01470


Theoretical massNumber of molelcules
Total (without water)16,5611
Polymers16,5611
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 At1g01470


Mass: 16560.988 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: O03983

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated ROESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM 15N,13C-labelled AT1g01470, 10mM phosphate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
NMRView5.1.0Johnsondata analysis
CNS1.1Brungerstructure solution
ARIA1.2Nilgesstructure solution
ARIA1.2Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle, cartesian coordinate dynamics; water refinement
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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