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- PDB-8gyn: zebrafish TIPE1 strucutre in complex with PE -

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Basic information

Entry
Database: PDB / ID: 8gyn
Titlezebrafish TIPE1 strucutre in complex with PE
ComponentsTumor necrosis factor alpha-induced protein 8-like protein 1
KeywordsLIPID BINDING PROTEIN / Lipid transfer protein / TIPE family
Function / homologyPI Metabolism / Tumor necrosis factor alpha-induced protein 8-like / Tumor necrosis factor alpha-induced protein 8-like superfamily / Tumor necrosis factor alpha-induced protein 8-like / negative regulation of TOR signaling / regulation of apoptotic process / cytoplasm / Chem-6OU / Tumor necrosis factor alpha-induced protein 8-like protein 1
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWang, W. / Cao, S.J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171207 China
National Natural Science Foundation of China (NSFC)31970584 China
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2023
Title: Structural insight into TIPE1 functioning as a lipid transfer protein.
Authors: Cao, S. / Zhang, Y. / Jiang, H. / Hou, X. / Wang, W.
History
DepositionSep 23, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor alpha-induced protein 8-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4062
Polymers18,6881
Non-polymers7181
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.080, 65.920, 35.490
Angle α, β, γ (deg.)90.000, 106.550, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Tumor necrosis factor alpha-induced protein 8-like protein 1 / TIPE1 / TNF alpha-induced protein 8-like protein 1 / TNFAIP8-like protein 1


Mass: 18687.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: tnfaip8l1, tnfaip8, si:dkey-49m19.6, zgc:55331 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SZE8
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M succinic acid, pH 7.0, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.38→34.02 Å / Num. obs: 30289 / % possible obs: 98.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2169 / CC1/2: 0.888 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4M

3f4m


Resolution: 1.38→25.66 Å / SU ML: 0.1161 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.3929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184 2000 6.61 %
Rwork0.1462 28268 -
obs0.1488 30268 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.77 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 49 203 1563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391438
X-RAY DIFFRACTIONf_angle_d0.61681933
X-RAY DIFFRACTIONf_chiral_restr0.061212
X-RAY DIFFRACTIONf_plane_restr0.0063245
X-RAY DIFFRACTIONf_dihedral_angle_d14.9341589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.25421310.17951954X-RAY DIFFRACTION94.77
1.42-1.460.20161450.16551953X-RAY DIFFRACTION97.99
1.46-1.50.23121250.14452015X-RAY DIFFRACTION97.18
1.5-1.550.18621460.13412026X-RAY DIFFRACTION98.82
1.55-1.60.18811540.1322007X-RAY DIFFRACTION99.59
1.6-1.670.19051370.12442008X-RAY DIFFRACTION99.58
1.67-1.740.17541450.13132062X-RAY DIFFRACTION99.95
1.74-1.840.1841390.13912015X-RAY DIFFRACTION99.81
1.84-1.950.18981490.14792034X-RAY DIFFRACTION99.54
1.95-2.10.16031480.15012049X-RAY DIFFRACTION99.5
2.1-2.310.18581440.14062037X-RAY DIFFRACTION99.36
2.31-2.650.19611450.15162032X-RAY DIFFRACTION99.54
2.65-3.330.19461420.15592023X-RAY DIFFRACTION98.59
3.33-25.660.17081500.14372053X-RAY DIFFRACTION98.22

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