[English] 日本語
Yorodumi
- PDB-9vr0: NMR solution structure of termini-truncated oxidized cytochrome c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vr0
TitleNMR solution structure of termini-truncated oxidized cytochrome c552 from Thioalkalivibrio paradoxus
ComponentsCytochrome c552
KeywordsELECTRON TRANSPORT / thiocyanate dehydrogenase electron acceptor / cytochrome c552 / class I cytochrome c / hemeprotein / periplasmic
Function / homologyCytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / electron transfer activity / heme binding / metal ion binding / HEME C / Cytochrome c552
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsBritikov, V.V. / Britikova, E.V. / Rakitina, T.V. / Dergousova, N.I. / Tikhonova, T.V. / Popov, V.O. / Bocharov, E.V.
Funding supportBelarus, Russian Federation, 2items
OrganizationGrant numberCountry
Belarusian Republican Foundation for Fundamental ResearchX23RSF-091Belarus
Russian Science Foundation23-44-10021 Russian Federation
CitationJournal: To Be Published
Title: NMR solution structure of termini-truncated oxidized cytochrome c552 from Thioalkalivibrio paradoxus
Authors: Britikov, V.V. / Britikova, E.V. / Rakitina, T.V. / Dergousova, N.I. / Tikhonova, T.V. / Popov, V.O. / Bocharov, E.V.
History
DepositionJul 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3912
Polymers13,7721
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 128structures with the lowest energy
RepresentativeModel #1medoid

-
Components

#1: Protein Cytochrome c552


Mass: 13772.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: WP_006748979.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8J0PCM1
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D HNCA
181isotropic13D HN(CO)CA
191isotropic13D HNCO
1101isotropic13D HCACO
1111isotropic13D HNHA
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D HN(CA)CB
1141isotropic13D HBHA(CO)NH
1151isotropic13D H(CCO)NH
1162isotropic12D 1H-1H NOESY
1172isotropic12D 1H-1H TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-100% 13C; U-100% 15N] Cytochrome c552, 50 mM sodium phosphate buffer, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
solution20.6 mM Cytochrome c552, 50 mM sodium phosphate buffer, 95% H2O/5% D2Ounlabeled_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCytochrome c552[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate buffernatural abundance1
0.6 mMCytochrome c552natural abundance2
50 mMsodium phosphate buffernatural abundance2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2.3Linge, O'Donoghue and Nilgeschemical shift assignment
CcpNmr Analysis2.5.2CCPNpeak picking
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 2 / Details: explicit water refinment
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 128 / 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