[English] 日本語
Yorodumi
- PDB-5zkv: Solution structure of molten globule state of L94G mutant of hors... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zkv
TitleSolution structure of molten globule state of L94G mutant of horse cytochrome-c
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Structure from MOLMOL
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / lipid binding / heme binding / metal ion binding ...cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / lipid binding / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsNaiyer, A. / Islam, A. / Hassan, M.I. / Sundd, M. / Ahmad, F.
CitationJournal: To Be Published
Title: Solution structure of molten globule state of L94G mutant of horse cytochrome-c
Authors: Naiyer, A. / Islam, A. / Hassan, M.I. / Sundd, M. / Ahmad, F.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Data collection / Database references
Category: database_2 / pdbx_database_related / pdbx_nmr_spectrometer
Item: _database_2.database_code / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2882
Polymers11,6691
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1120 Å2
ΔGint-22 kcal/mol
Surface area7040 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 2000structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Cytochrome c


Mass: 11669.492 Da / Num. of mol.: 1 / Mutation: L94G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P00004
#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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic13D C(CO)NH
191isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-15N TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic12D 1H-1H NOESY

-
Sample preparation

DetailsType: solution
Contents: 2 mM [U-99% 13C; U-99% 15N] Molten globule of L94G mutant of horse cytochrome-c, 90% H2O/10% D2O
Details: NMR sample comprised of 2 mM uniformly labelled (U-99% 13C; U-99% 15N) protein in 0.03 M cacodylate buffer containing 0.1 M NaCl (pH 6.0)
Label: U-99% 13C; U-99% 15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM
Component: Molten globule of L94G mutant of horse cytochrome-c
Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.03 M cacodylate buffer containing 0.1 M NaCl Not defined
Label: 2 mM uniformly labelled (U-99% 13C; U-99% 15N) protein in 0.03 M cacodylate buffer containing 0.1 M NaCl (pH 6.0)
pH: 6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

SoftwareName: CNS / Classification: refinement
NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 15

+
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