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- PDB-1yel: Structure of the hypothetical Arabidopsis thaliana protein At1g16640.1 -

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Basic information

Entry
Database: PDB / ID: 1yel
TitleStructure of the hypothetical Arabidopsis thaliana protein At1g16640.1
ComponentsAt1g16640
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CESG / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


DNA binding / nucleus
Similarity search - Function
: / DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
B3 domain-containing protein At1g16640
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent.
AuthorsPeterson, F.C. / Waltner, J.K. / Lytle, B.L. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2005
Title: Structure of the B3 domain from Arabidopsis thaliana protein At1g16640
Authors: Waltner, J.K. / Peterson, F.C. / Lytle, B.L. / Volkman, B.F.
History
DepositionDec 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: At1g16640


Theoretical massNumber of molelcules
Total (without water)12,1801
Polymers12,1801
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 #1closest to the average

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Components

#1: Protein At1g16640


Mass: 12179.882 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: Q9FX77

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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
1313D 13C-separated NOESY (aromatic)
NMR detailsText: All triple-resonance and NOESY spectra were acquired using a cryogenic probe.

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Sample preparation

DetailsContents: 0.8 mM At1g16640 U-15N,13C, 20 mM PO4, 50 mM NaCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70 mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
NMRPipe2004Frank Delaglioprocessing
SPSCANRalf Glaserdata analysis
XEASY1.3data analysis
GARANT2.1data analysis
CYANA1.0.6Peter Guntertstructure solution
X-PLORNIHG. Marius Clorerefinement
RefinementMethod: Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent.
Software ordinal: 1
Details: Structures are based on a total of 1294 NOE restraints (241 intra, 301 sequential, 193 medium, and 559 long range), and 144 phi and psi dihedral angle constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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