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- PDB-9kyi: Crystal structure of mouse Endothelial-overexpressed lipopolysacc... -

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Basic information

Entry
Database: PDB / ID: 9kyi
TitleCrystal structure of mouse Endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1)
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: 1.55 Å
AuthorsGuo, W.T. / Meng, C.Y. / Wen, Y. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of mouse Endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1)
Authors: Guo, W.T. / Meng, C.Y. / Wen, Y. / Wu, B.X.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein EOLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3573
Polymers18,1651
Non-polymers1922
Water3,585199
1
A: Protein EOLA1
hetero molecules

A: Protein EOLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7146
Polymers36,3302
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area2560 Å2
ΔGint-65 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.252, 50.943, 96.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

21A-495-

HOH

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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: 18164.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first serine is from tag / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.21 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97736 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 24456 / % possible obs: 99.7 % / Redundancy: 21.1 % / Biso Wilson estimate: 11.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.017 / Rrim(I) all: 0.187 / Net I/σ(I): 6.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2333 / CC1/2: 0.986 / Rpim(I) all: 0.05 / Rrim(I) all: 0.187 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→27.85 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 18.4036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 1230 5.04 %
Rwork0.1746 23179 -
obs0.1758 24409 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.52 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 10 199 1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061327
X-RAY DIFFRACTIONf_angle_d0.86181809
X-RAY DIFFRACTIONf_chiral_restr0.0551204
X-RAY DIFFRACTIONf_plane_restr0.0064228
X-RAY DIFFRACTIONf_dihedral_angle_d19.1245499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.22841170.18342474X-RAY DIFFRACTION97.26
1.61-1.690.20511290.18052547X-RAY DIFFRACTION99.93
1.69-1.770.19061280.18022542X-RAY DIFFRACTION100
1.77-1.890.19611330.17892549X-RAY DIFFRACTION99.96
1.89-2.030.20271410.17772559X-RAY DIFFRACTION99.96
2.03-2.240.18541440.17142573X-RAY DIFFRACTION100
2.24-2.560.20531390.1752578X-RAY DIFFRACTION99.89
2.56-3.220.22251500.1822604X-RAY DIFFRACTION100
3.22-27.850.17991490.16562753X-RAY DIFFRACTION99.93

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