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- PDB-2g0q: Solution structure of At5g39720.1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2g0q
TitleSolution structure of At5g39720.1 from Arabidopsis thaliana
ComponentsAT5G39720.1 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / At5g39720.1 / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #210 / Protein AIG2-like / Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #210 / Protein AIG2-like / Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Roll / Alpha Beta
Similarity search - Domain/homology
: / AIG2-like protein A
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
AuthorsVolkman, B.F. / Peterson, F.C. / Lytle, B.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family.
Authors: Lytle, B.L. / Peterson, F.C. / Tyler, E.M. / Newman, C.L. / Vinarov, D.A. / Markley, J.L. / Volkman, B.F.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 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: AT5G39720.1 protein


Theoretical massNumber of molelcules
Total (without water)20,1271
Polymers20,1271
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 #1lowest energy

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Components

#1: Protein AT5G39720.1 protein


Mass: 20126.820 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: At5g39720.1 / Plasmid: pEU-HIS / References: GenBank: 15242449, UniProt: Q9FIX2*PLUS

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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 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: 0.9 mM At5g39720.1 U-15N/13C, 10 mM deuterated Bis-Tris, 100 mM NaCl, 5 mM Dithiothreitol, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 101 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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.3SCHWIETERS, C.D.,KUSZEWSKI, J.J.,TJANDRA, N., CLORE, G.M.refinement
XwinNMR3.5collection
NMRPipe2004processing
SPSCAN1.1.0data analysis
XEASY1.3data analysis
GARANT2.1data analysis
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 1989 NOE CONSTRAINTS ( 522 INTRA, 564 SEQEUNTIAL, 267 MEDIUM and 636 LONG RANGE CONSTRAINTS) AND 189 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
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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