[English] 日本語
Yorodumi
- PDB-2jsp: The prokaryotic Cys2His2 zinc finger adopts a novel fold as revea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jsp
TitleThe prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A. tumefaciens Ros DNA binding domain
ComponentsTranscriptional regulatory protein ros
KeywordsGENE REGULATION / prokaryotic Cys2His2 zinc finger
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
ROS/MUCR transcriptional regulator protein / ROS/MUCR transcriptional regulator / ROS/MUCR transcriptional regulator superfamily / ROS/MUCR transcriptional regulator protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein ros
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMalgieri, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
Authors: Malgieri, G. / Russo, L. / Esposito, S. / Baglivo, I. / Zaccaro, L. / Pedone, E.M. / Di Blasio, B. / Isernia, C. / Pedone, P.V. / Fattorusso, R.
History
DepositionJul 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: Transcriptional regulatory protein ros


Theoretical massNumber of molelcules
Total (without water)9,9541
Polymers9,9541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Transcriptional regulatory protein ros


Mass: 9954.439 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: ros / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / References: UniProt: Q04152

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1322D 1H-13C HSQC
1432D 1H-1H NOESY
1523D CBCA(CO)NH
1623D CBCANH
1723D HNCO
1823D HNCA
1913D HNHA
11023D 1H-13C NOESY
11113D 1H-15N NOESY
11223D CCH-TOCSY
11313D 1H-15N TOCSY
11432D 1H-1H TOCSY
11522D 1H-15N HSQC IPAP
11622D 1H-15N HSQC IPAP

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Ros87, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Ros87, 90% H2O/10% D2O90% H2O/10% D2O
31 mM Ros87, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRos87[U-100% 15N]1
1 mMRos87[U-100% 13C; U-100% 15N]2
1 mMRos873
Sample conditionsIonic strength: 0.2 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE8004

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
XEASYBartels, C. et al.data analysis
Procheck-NMRLaskowski, R.A. et al.data analysis
ModelFreePalmer III, A.G. et al.data analysis
MOLMOLKoradi, R. et al.data analysis
SPDBGuex, N. et al.data analysis
CYANAGuntert, P. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
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