[English] 日本語
Yorodumi
- PDB-9kyj: Crystal structure of mouse Endothelial-overexpressed lipopolysacc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kyj
TitleCrystal structure of mouse Endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1), Selenomethionine derivative
ComponentsProtein EOLA1
KeywordsIMMUNE SYSTEM / ASCH domain
Function / homologyProtein EOLA1/EOLA2 / ASCH / ASCH domain / ASCH domain / PUA-like superfamily / Protein EOLA1
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsGuo, W.T. / Meng, C.Y. / Wen, Y. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.
Authors: Meng, C. / Shi, X. / Guo, W. / Jian, X. / Zhao, J. / Wen, Y. / Wang, R. / Li, Y. / Xu, S. / Chen, H. / Zhang, J. / Chen, M. / Chen, H. / Wu, B.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein EOLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5944
Polymers18,3061
Non-polymers2883
Water3,513195
1
A: Protein EOLA1
hetero molecules

A: Protein EOLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1888
Polymers36,6112
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2890 Å2
ΔGint-93 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.128, 96.102, 33.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-493-

HOH

-
Components

#1: Protein Protein EOLA1 / Endothelial-overexpressed lipopolysaccharide-associated factor 1 / Endothelium and lymphocyte ...Endothelial-overexpressed lipopolysaccharide-associated factor 1 / Endothelium and lymphocyte associated ASCH domain 1


Mass: 18305.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eola1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D1F3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 23707 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 3.2
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2320 / CC1/2: 0.961 / Rpim(I) all: 0.103 / Rrim(I) all: 0.368 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→45.14 Å / SU ML: 0.1583 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.3102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 1203 5.09 %
Rwork0.1825 22429 -
obs0.1839 23632 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.38 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 15 195 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611331
X-RAY DIFFRACTIONf_angle_d0.85661815
X-RAY DIFFRACTIONf_chiral_restr0.0555204
X-RAY DIFFRACTIONf_plane_restr0.0064228
X-RAY DIFFRACTIONf_dihedral_angle_d19.8429499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.630.28071410.21142401X-RAY DIFFRACTION98.76
1.63-1.710.26221250.19982452X-RAY DIFFRACTION99.85
1.71-1.80.24321380.1892450X-RAY DIFFRACTION99.88
1.8-1.910.2021250.18872466X-RAY DIFFRACTION99.88
1.91-2.060.21631360.17972469X-RAY DIFFRACTION99.88
2.06-2.260.22831210.17992504X-RAY DIFFRACTION99.92
2.26-2.590.20561240.18952512X-RAY DIFFRACTION100
2.59-3.260.20841360.18892522X-RAY DIFFRACTION99.89
3.26-45.140.18271570.16672653X-RAY DIFFRACTION99.93

+
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