[English] 日本語
Yorodumi
- PDB-2k7i: Solution NMR structure of protein ATU0232 from AGROBACTERIUM TUME... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k7i
TitleSolution NMR structure of protein ATU0232 from AGROBACTERIUM TUMEFACIENS. Northeast Structural Genomics Consortium (NESG) target AtT3. Ontario Center for Structural Proteomics target ATC0223.
ComponentsUPF0339 protein Atu0232
Keywordsstructural genomics / unknown function / protein of unknown function / swapped dimer. PSI2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYegP-like / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / UPF0339 protein Atu0232
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Srisailam, S. / Yee, A. / Bansal, S. / Semesi, A. / Prestegard, J. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution structure of protein ATU0232 from Agrobacterium Tumefaciens.
Authors: Lemak, A. / Srisailam, S. / Yee, A. / Bansal, S. / Semesi, A. / Prestegard, J. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionAug 12, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0339 protein Atu0232
B: UPF0339 protein Atu0232


Theoretical massNumber of molelcules
Total (without water)18,7552
Polymers18,7552
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein UPF0339 protein Atu0232


Mass: 9377.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: tumefaciens / Strain: C58 / Gene: Atu0232, AGR_C_390 / Plasmid: p15Tv lic / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UIR1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)C(CO)NH TOCSY
1613D H(CCO)NH TOCSY
1723D (H)CCH-TOCSY
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11123D 1H-13C NOESY
11213D 1H-13C arom NOESY
11312D 1H-15N HSQC(IPAP)

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] Atu0232, 10 mM TRIS, 500 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM Benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] Atu0232, 10 mM TRIS, 500 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM Benzamidine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtu0232[U-13C; U-15N]1
10 mMTRIS1
500 mMsodium chloride1
10 uMZnSO41
10 mMDTT1
0.01 %NaN31
10 mMBenzamidine1
0.5 mMAtu0232[U-13C; U-15N]2
10 mMTRIS2
500 mMsodium chloride2
10 uMZnSO42
10 mMDTT2
0.01 %NaN32
10 mMBenzamidine2
Sample conditionsIonic strength: 500 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Llinas, Arrowsmithresonance assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: molecular dynamics in water bath with RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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://pdbjlvh1.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