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- PDB-5y7d: Crystal structure of human Endothelial-overexpressed LPS associat... -

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Basic information

Entry
Database: PDB / ID: 5y7d
TitleCrystal structure of human Endothelial-overexpressed LPS associated factor 1
ComponentsProtein CXorf40A
KeywordsHYDROLASE / endothelial-overexpressed LPS associated factor 1 / RNA binding domain / PUA domain
Function / homologyProtein EOLA1/EOLA2 / ASCH / ASCH domain / regulation of interleukin-6 production / PUA-like superfamily / regulation of gene expression / Protein EOLA1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsPark, S.H. / Kim, M.J. / Park, J.S. / Kim, H.J. / Han, B.W.
CitationJournal: Molecules / Year: 2019
Title: Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding.
Authors: Kim, M. / Park, S.H. / Park, J.S. / Kim, H.J. / Han, B.W.
History
DepositionAug 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CXorf40A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,86117
Polymers18,2431
Non-polymers61816
Water3,981221
1
A: Protein CXorf40A
hetero molecules

A: Protein CXorf40A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72334
Polymers36,4862
Non-polymers1,23632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4060 Å2
ΔGint-140 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.765, 49.765, 175.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-464-

HOH

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Components

#1: Protein Protein CXorf40A / Endothelial-overexpressed lipopolysaccharide-associated factor 1


Mass: 18243.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXorf40A, CXorf40, EOLA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TE69
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 4.3M NaCl

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.709→47.89 Å / Num. obs: 24918 / % possible obs: 99.8 % / Redundancy: 29.4 % / Net I/σ(I): 53.11

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.71→32.933 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2469 1238 4.98 %
Rwork0.1994 --
obs0.2017 24868 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→32.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 26 221 1530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041321
X-RAY DIFFRACTIONf_angle_d0.7031789
X-RAY DIFFRACTIONf_dihedral_angle_d10.03794
X-RAY DIFFRACTIONf_chiral_restr0.051200
X-RAY DIFFRACTIONf_plane_restr0.004230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7096-1.77810.24981400.24642545X-RAY DIFFRACTION100
1.7781-1.8590.28481350.23732562X-RAY DIFFRACTION100
1.859-1.9570.27591330.22982574X-RAY DIFFRACTION100
1.957-2.07960.29121460.21312579X-RAY DIFFRACTION100
2.0796-2.24010.27181240.20342589X-RAY DIFFRACTION100
2.2401-2.46550.26181540.21082607X-RAY DIFFRACTION100
2.4655-2.82210.25541310.22012643X-RAY DIFFRACTION100
2.8221-3.55490.24711470.19352687X-RAY DIFFRACTION100
3.5549-32.93880.21171280.17572844X-RAY DIFFRACTION99

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