[English] 日本語
Yorodumi
- PDB-2m7a: Enteropathogenic Escherichia coli 0111:H- str. 11128 ORF EC0111_1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m7a
TitleEnteropathogenic Escherichia coli 0111:H- str. 11128 ORF EC0111_1119 similar to bacteriophage lambda ea8.5
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / bacteriophage / zinc binding / CHCC motif
Function / homologyArc Repressor Mutant, subunit A - #1920 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsDonaldson, L.W.F.
CitationJournal: Biochemistry / Year: 2013
Title: The Solution Structures of Two Prophage Homologues of the Bacteriophage lambda Ea8.5 Protein Reveal a Newly Discovered Hybrid Homeodomain/Zinc-Finger Fold.
Authors: Kwan, J.J. / Smirnova, E. / Khazai, S. / Evanics, F. / Maxwell, K.L. / Donaldson, L.W.
History
DepositionApr 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3922
Polymers11,3271
Non-polymers651
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein


Mass: 11326.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: locus AP010960 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O111:H- / Description: codon optimized synthetic gene / Gene: EC0111_1119, ECO111_1119 / Variant: 11128 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C8UME7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: The structure of this gene product is a hybrid of a homeodomain fold and a helix-strand-strand zinc binding domain. Amino acids 1-15 are ununstructured. The loop of the helix-loop-helix ...Details: The structure of this gene product is a hybrid of a homeodomain fold and a helix-strand-strand zinc binding domain. Amino acids 1-15 are ununstructured. The loop of the helix-loop-helix motif from aa. 58-69 is unstructured. Amino acids 95-99 (to the native C-terminus) are unstructured.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1213D HN(CA)CB
131CBCA(CO)NH (H[N[co[{CA|ca[C]}]]])
1413D HNCO
151HN(CA)CO (H[N[ca[CO]]])
1613D HBHA(CO)NH
1712D 1H-13C HSQC aliphatic
1812D 1H-13C HSQC aromatic
1913D (H)CCH-TOCSY
11013D H(CCO)NH
11113D C(CO)NH
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11412D CBHD
11512D CBHE

-
Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] Molecule 1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: Molecule 1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.150 / pH: 7.800 / Pressure: 1.000 atm / Temperature: 289.000 K

-
NMR measurement

NMR spectrometerType: Varian Varian / Manufacturer: Varian / Model: Varian / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNpeak picking
CcpNmr Analysis2.2CCPNrestraint calculation
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 943 / NOE intraresidue total count: 411 / NOE long range total count: 130 / NOE medium range total count: 107 / NOE sequential total count: 272 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 69
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.3557 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 2.28 ° / Maximum upper distance constraint violation: 0.04 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.0226 Å / Distance rms dev error: 0.0004 Å

+
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