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- PDB-1wvk: NMR Solution Structure of the Partially Disordered Protein At2g23... -

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Basic information

Entry
Database: PDB / ID: 1wvk
TitleNMR Solution Structure of the Partially Disordered Protein At2g23090 from Arabidopsis thaliana
ComponentsAt2g23090/F21P24.15
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / PSI / cell free / Center for Eukaryotic Structural Genomics / CESG / At2g23090.1
Function / homology
Function and homology information


At2g23090 / At2g23090-like / Uncharacterised protein family SERF, N-terminal / ZNF706/At2g23090 superfamily / At2g23090-like, zinc-binding domain / At2g23090-like / Small EDRK-rich factor 1/2-like, N-terminal / Zinc-binding / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Uncharacterized protein At2g23090
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics, water refinement
AuthorsTyler, R.C. / Tonelli, M. / Lee, M. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: NMR Solution Structure of the Partially Disordered Protein At2g23090 from Arabidopsis thaliana
Authors: Tyler, R.C. / Tonelli, M. / Lee, M. / Markley, J.L.
History
DepositionDec 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: At2g23090/F21P24.15


Theoretical massNumber of molelcules
Total (without water)9,3911
Polymers9,3911
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)15 / 15structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein At2g23090/F21P24.15


Mass: 9390.949 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: AT2G23090 / Plasmid: PEU-HIS / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: O64818

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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

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Sample preparation

DetailsContents: 1mM At2g23090 U-13C, U-15N; 10mM Bis-Tris buffer, 100mM NaCl, 90% H2O, 10% D2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 100mM NaCl / pH: 5.8 / Pressure: ambient / Temperature: 300 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 INOVAVarianINOVA9001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Nilges, M.structure solution
ARIA1.2Nilges, M.refinement
RefinementMethod: simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics, water refinement
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 15 / Conformers submitted total number: 15

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