[English] 日本語
Yorodumi
- PDB-2l49: The solution structure of the P2 C,the immunity repressor of the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l49
TitleThe solution structure of the P2 C,the immunity repressor of the P2 bacteriophage
ComponentsC protein
KeywordsDNA BINDING PROTEIN / P2 bacteriophage / P2 C / direct repeats / DNA-binding protein
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Repressor protein C / C protein
Similarity search - Component
Biological speciesEnterobacteria phage P2 (virus)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsMassad, T. / Papadopolos, E. / Stenmark, P. / Damberg, P.
CitationJournal: J.Biomol.Nmr / Year: 2016
Title: The C repressor of the P2 bacteriophage.
Authors: Massad, T. / Papadopolos, E. / Stenmark, P. / Damberg, P.
History
DepositionOct 1, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C protein
B: C protein


Theoretical massNumber of molelcules
Total (without water)22,0532
Polymers22,0532
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein C protein


Mass: 11026.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: C / Production host: Escherichia coli (E. coli) / References: UniProt: Q83VS7, UniProt: P04132*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HBHA(CO)NH
11013D HN(CO)CA

-
Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] entity-1, 10 % D2O-2, 10 mM sodium phosphate-3, 1 mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity-1[U-100% 13C; U-100% 15N]1
10 %D2O-21
10 mMsodium phosphate-31
1 mMDTT-41
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE5004
Varian INOVAVarianINOVA6005

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Braun and Wuthrichstructure solution
CYANA2.1Guntert, Braun and Wuthrichchemical shift assignment
CYANA2.1Guntert, Braun and Wuthrichprocessing
CYANA2.1Guntert, Braun and Wuthrichchemical shift calculation
CYANA2.1Guntert, Braun and Wuthrichgeometry optimization
CYANA2.1Goddardstructure solution
CYANA2.1Goddardchemical shift assignment
CYANA2.1Goddardprocessing
CYANA2.1Goddardchemical shift calculation
CYANA2.1Goddardgeometry optimization
CYANA2.1Bruker Biospinstructure solution
CYANA2.1Bruker Biospinchemical shift assignment
CYANA2.1Bruker Biospinprocessing
CYANA2.1Bruker Biospinchemical shift calculation
CYANA2.1Bruker Biospingeometry optimization
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxgeometry optimization
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 130 / Protein psi angle constraints total count: 130
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://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