[English] 日本語
Yorodumi
- PDB-1lm0: Solution structure and characterization of the heme chaperone CcmE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lm0
TitleSolution structure and characterization of the heme chaperone CcmE
Componentscytochrome c maturation protein E
KeywordsCHAPERONE / all-beta protein / heme delivery / cytochrome c maturation / OB-(oligonucleotide binding)fold
Function / homology
Function and homology information


cytochrome complex assembly / heme binding / metal ion binding / plasma membrane
Similarity search - Function
CcmE/CycJ protein / CcmE-like superfamily / CcmE domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cytochrome c-type biogenesis protein CcmE / Cytochrome c-type biogenesis protein CcmE
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dyanamics, restrained energy minimization
AuthorsArnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure and characterization of the heme chaperone CcmE
Authors: Arnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cytochrome c maturation protein E


Theoretical massNumber of molelcules
Total (without water)14,7141
Polymers14,7141
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)35 / 400the submitted conformer models are the 35 structures with the lowest target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein cytochrome c maturation protein E


Mass: 14714.397 Da / Num. of mol.: 1 / Fragment: water soluble domain of CcmE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: ccmE / Plasmid: pPB10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3) / References: UniProt: O52690, UniProt: Q8EK44*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
151HNHA
161HNCO
171HNHB
181CBCANH
191CC(CO)NH
1101CBCA(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy on 13C and 15N double labeled apoCcmE.

-
Sample preparation

DetailsContents: 2.0 mM apoCcmE, 20 mM phosphate, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM phosphate / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3Xia, Bartelsdata analysis
DYANA1.5Gunter, Mumenthaler, Wuthrichstructure solution
CORMABorgias, Thomas, Jamesiterative matrix relaxation
Amber5Pearlman, Case, Caldwell, Ross, Cheatham, Ferguson, Seibel, Singh, Weiner, Kollmanrefinement
RefinementMethod: simulated annealing, torsion angle dyanamics, restrained energy minimization
Software ordinal: 1
Details: 1866 meaningful NOEs and 89 dihedral angle constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: the submitted conformer models are the 35 structures with the lowest target function
Conformers calculated total number: 400 / Conformers submitted total number: 35

+
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