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- PDB-5jxd: Crystal structure of murine Tnfaip8 C165S mutant -

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Basic information

Entry
Database: PDB / ID: 5jxd
TitleCrystal structure of murine Tnfaip8 C165S mutant
ComponentsTumor necrosis factor alpha-induced protein 8
KeywordsIMMUNE SYSTEM / Tnfaip8 / Oxi-a / phosphatidylethanolamine
Function / homology
Function and homology information


PI Metabolism / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / defense response to Gram-positive bacterium / positive regulation of apoptotic process / nucleoplasm / cytoplasm
Similarity search - Function
Tumor necrosis factor alpha-induced protein 8-like / Tumor necrosis factor alpha-induced protein 8-like / Tumor necrosis factor alpha-induced protein 8-like superfamily / Domain of unknown function (DUF758) / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6OU / Tumor necrosis factor alpha-induced protein 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.029 Å
AuthorsPark, J. / Kim, M.S. / Lee, D. / Shin, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education, Science and Technology2010K000266 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2017
Title: The Tnfaip8-PE complex is a novel upstream effector in the anti-autophagic action of insulin
Authors: Kim, J.S. / Park, J. / Kim, M.S. / Ha, J.Y. / Jang, Y.W. / Shin, D.H. / Son, J.H.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tumor necrosis factor alpha-induced protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6992
Polymers22,9811
Non-polymers7181
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10740 Å2
Unit cell
Length a, b, c (Å)66.276, 71.570, 90.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Tumor necrosis factor alpha-induced protein 8 / TNF alpha-induced protein 8


Mass: 22981.432 Da / Num. of mol.: 1 / Mutation: C165S / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q921Z5
#2: Chemical ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 0.1M Bis-Tris propane, pH 7.7, 1.2M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.029→33.14 Å / Num. obs: 13998 / % possible obs: 97.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 23.15
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.58 / % possible all: 74.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4M

3f4m


Resolution: 2.029→33.138 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 699 5 %
Rwork0.2372 --
obs0.2395 13973 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.029→33.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 49 21 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081590
X-RAY DIFFRACTIONf_angle_d1.7022125
X-RAY DIFFRACTIONf_dihedral_angle_d19.6624
X-RAY DIFFRACTIONf_chiral_restr0.096240
X-RAY DIFFRACTIONf_plane_restr0.005267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0291-2.18580.30471470.28962376X-RAY DIFFRACTION90
2.1858-2.40570.25691220.24752667X-RAY DIFFRACTION99
2.4057-2.75370.28971510.24182687X-RAY DIFFRACTION100
2.7537-3.46870.29831560.25022691X-RAY DIFFRACTION100
3.4687-33.14240.28251230.22222853X-RAY DIFFRACTION100

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