[English] 日本語
Yorodumi
- PDB-2g0q: Solution structure of At5g39720.1 from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #210 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT5G39720.1 protein


Theoretical massNumber of molelcules
Total (without water)20,1271
Polymers20,1271
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

-
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

-
Experimental details

-
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.

-
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: 7.0 / Pressure: AMBIENT / Temperature: 298 K

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more