[English] 日本語
Yorodumi
- PDB-9gsa: Lys9DabMC6*a 1-Delta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gsa
TitleLys9DabMC6*a 1-Delta
Components
  • ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2
  • ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2
KeywordsDE NOVO PROTEIN / ALPHA-HELIX / DESIGN / MINIATURIZED METALLOPROTEINS
Function / homologyCO(III)-(DEUTEROPORPHYRIN IX) / HYDROXIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsMaglio, O. / Lombardi, A. / Chino, M. / Pirro, F.
Funding support2items
OrganizationGrant numberCountry
Other government
Other government
Citation
Journal: Inorganic Chemistry / Year: 2026
Title: Iron to cobalt swapping in a bioinspired heme-peroxidase: structural characterization and functional implications
Authors: Chino, M. / Cerrone, C. / Pirro, F. / De Fenza, M. / Demeshko, S. / Maglio, O. / Meyer, F. / Lombardi, A.
#1: Journal: Chem. Comm. / Year: 2021
Title: Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts
Authors: Maglio, O. / Chino, M. / Vicari, C. / Pavone, V. / Louro, R.O. / Lombardi, A.
#2: Journal: Chemistry / Year: 2003
Title: Design of a new mimochrome with unique topology.
Authors: Lombardi, A. / Nastri, F. / Marasco, D. / Maglio, O. / De Sanctis, G. / Sinibaldi, F. / Santucci, R. / Coletta, M. / Pavone, V.
History
DepositionSep 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2
B: ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4914
Polymers2,9062
Non-polymers5852
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2


Mass: 1170.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2


Mass: 1736.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-DEU / CO(III)-(DEUTEROPORPHYRIN IX)


Mass: 567.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28CoN4O4 / 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-1H NOESY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY

-
Sample preparation

DetailsType: solution / Contents: 0.20 mM None MC6*a 1-Delta, 60% H2O/40% TFE / Label: None / Solvent system: 60% H2O/40% TFE
SampleConc.: 0.20 mM / Component: MC6*a 1-Delta / Isotopic labeling: None
Sample conditionsIonic strength: trifluoraocetate Not defined / Label: 1 / pH: 4.6 pD / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: with cryo-probe

-
Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber10Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
Details: CYANA structures with the lowest target function were subjected to restrained molecular dynamics (RMD) and restrained energy minimization (REM) with the Sander module of the AMBER 10.0 package
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / 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