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- PDB-1yyc: Solution Structure of a putative late embryogenesis abundant (LEA... -

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Basic information

Entry
Database: PDB / ID: 1yyc
TitleSolution Structure of a putative late embryogenesis abundant (LEA) protein At2g46140.1
Componentsputative late embryogenesis abundant proteinLate embryogenesis abundant proteins
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / CESG / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


response to desiccation / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #1820 / Late embryogenesis abundant protein, LEA_2 subgroup / Water stress and hypersensitive response domain / Late embryogenesis abundant protein / Water Stress and Hypersensitive response / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich ...Immunoglobulin-like - #1820 / Late embryogenesis abundant protein, LEA_2 subgroup / Water stress and hypersensitive response domain / Late embryogenesis abundant protein / Water Stress and Hypersensitive response / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Desiccation-related protein At2g46140
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsCenter for Eukaryotic Structural Genomics (CESG) / Song, J. / Tyler, R.C. / Lee, M.S. / Markley, J.L.
CitationJournal: To be Published
Title: Solution Structure of a putative late embryogenesis abundant (LEA) protein At2g46140.1
Authors: Song, J. / Tyler, R.C. / Lee, M.S. / Markley, J.L.
History
DepositionFeb 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: 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: putative late embryogenesis abundant protein


Theoretical massNumber of molelcules
Total (without water)18,8591
Polymers18,8591
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 putative late embryogenesis abundant protein / Late embryogenesis abundant proteins / LEA protein


Mass: 18859.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: At2g46140 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: O82355

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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
141HN(CO)CACB
151HCCHTOCSY
161C(CO)NH

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Sample preparation

DetailsContents: 10 mM Bis-Tris, 100 mM NaCl,10 mM DTT, pH 7.0, 90% H2O,10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.0 / 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
Bruker DMXBrukerDMX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe97.027.12.56Delaglio et al.processing
Sparky3.72Goddard T.D. and Kneller, D.G.data analysis
CYANA1.0.6Guntert et alstructure solution
XPLOR-NIH2.9.3Schwieters, C.D. et alrefinement
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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