[English] 日本語
Yorodumi
- PDB-9ejv: Co-MAHF-9 A8R Metal Alpha-Helix Framework -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ejv
TitleCo-MAHF-9 A8R Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8R
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsRichardson-Matthews, R.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM15479301 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Metal-alpha-Helix Peptide Frameworks.
Authors: Richardson-Matthews, R. / Velko, K. / Bhunia, B. / Ghosh, S. / Oktawiec, J. / Brunzelle, J.S. / Dang, V.T. / Nguyen, A.I.
History
DepositionNov 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Co-MAHF-9 A8R
B: Co-MAHF-9 A8R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4336
Polymers2,1232
Non-polymers3104
Water46826
1
A: Co-MAHF-9 A8R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2533
Polymers1,0611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8R
hetero molecules


  • defined by author&software
  • 1.18 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1793
Polymers1,0611
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.682, 16.260, 24.696
Angle α, β, γ (deg.)99.610, 97.480, 107.030
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein/peptide Co-MAHF-9 A8R


Mass: 1061.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.28 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: water, acetonitrile, cobalt acetate, sodium hydroxide, methanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.688801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688801 Å / Relative weight: 1
ReflectionResolution: 0.92→15.18 Å / Num. obs: 9050 / % possible obs: 93.38 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 0.92→0.9531 Å / Num. unique obs: 928 / CC1/2: 0.71

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.92→15.18 Å / SU ML: 0.0731 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 14.0806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1348 1643 9.9 %
Rwork0.1132 14946 -
obs0.1153 9050 85.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.32 Å2
Refinement stepCycle: LAST / Resolution: 0.92→15.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms144 0 20 26 190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066156
X-RAY DIFFRACTIONf_angle_d1.606216
X-RAY DIFFRACTIONf_chiral_restr0.051118
X-RAY DIFFRACTIONf_plane_restr0.011122
X-RAY DIFFRACTIONf_dihedral_angle_d21.874424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.950.26081160.23241230X-RAY DIFFRACTION83.4
0.95-0.980.24321380.20791237X-RAY DIFFRACTION84.15
0.98-1.010.21731440.17491230X-RAY DIFFRACTION83.27
1.01-1.050.17981330.17421255X-RAY DIFFRACTION87.74
1.05-1.10.19461280.14561245X-RAY DIFFRACTION84.86
1.1-1.160.13651550.12951239X-RAY DIFFRACTION86.05
1.16-1.230.14361340.11281260X-RAY DIFFRACTION86.8
1.23-1.330.11561560.10591248X-RAY DIFFRACTION87.75
1.33-1.460.13831420.10421282X-RAY DIFFRACTION88.89
1.47-1.670.12021370.08931239X-RAY DIFFRACTION91.01
1.67-2.10.09471240.08691242X-RAY DIFFRACTION84.32
2.11-15.180.0951360.07961239X-RAY DIFFRACTION85.3

+
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