[English] 日本語
Yorodumi
- PDB-1k3g: NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k3g
TitleNMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii
Componentscytochrome c-553
KeywordsELECTRON TRANSPORT / C-553 / HEME / CYTOCHROME / BACILLUS PASTEURII / ELECTRON TRANSFER
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome c, Bacillus subtilis c550-related / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-553
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, restrained energy minimization
AuthorsBanci, L. / Bertini, I. / Ciurli, S. / Dikiy, A. / Dittmer, J. / Rosato, A. / Sciara, G. / Thompsett, A.R.
Citation
Journal: Chembiochem / Year: 2002
Title: NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
Authors: Banci, L. / Bertini, I. / Ciurli, S. / Dikiy, A. / Dittmer, J. / Rosato, A. / Sciara, G. / Thompsett, A.R.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal Structure of Oxidized Bacillus pasteurii cytochrome c-553 at 0.97-A Resolution
Authors: Benini, S. / Gonzalez, A. / Rypniewski, W.R. / Wilson, K.S. / Van Beeumen, J.J. / Ciurli, S.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: Modulation of Bacillus pasteurii Cytochrome c553 Reduction Potential by Structural and Solution Parameters
Authors: Benini, S. / Borsari, M. / Ciurli, S. / Dikiy, A. / Lamborghini, M.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_conn / struct_conn_type / 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_nmr_spectrometer.model / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cytochrome c-553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7342
Polymers7,1161
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 400target function
Representative

-
Components

#1: Protein cytochrome c-553 / C553


Mass: 7115.937 Da / Num. of mol.: 1 / Fragment: residues 22-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporosarcina pasteurii (bacteria) / Plasmid: pEC86 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P82599
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121HNHA
1311D NOE

-
Sample preparation

DetailsContents: 1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer
Solvent system: 90%H2O+10%D2O; 100% D2O
Sample conditionsIonic strength: 10 mM phosphate buffer / pH: 7.5 / Pressure: Ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3.13Xiadata analysis
DYANA1.5Guentertstructure solution
Amber5Kollmanrefinement
RefinementMethod: torsion angle dynamics, restrained energy minimization
Software ordinal: 1
Details: PSEUDOCONTACT SHIFTS WERE INCLUDED AS CONSTRAINTS BY MEANS OF MODIFIED DYANA AND SANDER MODULES (PSEUDODYANA, PSEUDOREM) (BANCI ET AL., 1997)
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 30

+
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