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- PDB-4q9v: Crystal structure of TIPE3 -

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Basic information

Entry
Database: PDB / ID: 4q9v
TitleCrystal structure of TIPE3
ComponentsTumor necrosis factor alpha-induced protein 8-like protein 3
KeywordsIMMUNE SYSTEM / helix / lipid transfer protein
Function / homology
Function and homology information


1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process / PI Metabolism / phosphatidylinositol transfer activity / phospholipid transport / phospholipid metabolic process / phosphatidylinositol binding / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / nucleoplasm / plasma membrane ...1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process / PI Metabolism / phosphatidylinositol transfer activity / phospholipid transport / phospholipid metabolic process / phosphatidylinositol binding / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / nucleoplasm / plasma membrane / cytosol / 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
Tumor necrosis factor alpha-induced protein 8-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, J. / Zhang, X. / Chen, Y.H. / Shi, Y.
CitationJournal: Cancer Cell / Year: 2014
Title: TIPE3 Is the Transfer Protein of Lipid Second Messengers that Promote Cancer.
Authors: Fayngerts, S.A. / Wu, J. / Oxley, C.L. / Liu, X. / Vourekas, A. / Cathopoulis, T. / Wang, Z. / Cui, J. / Liu, S. / Sun, H. / Lemmon, M.A. / Zhang, L. / Shi, Y. / Chen, Y.H.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-like protein 3
B: Tumor necrosis factor alpha-induced protein 8-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,22415
Polymers43,2782
Non-polymers94613
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-147 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.729, 87.296, 242.309
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-like protein 3 / TNF alpha-induced protein 8-like protein 3 / TNFAIP8-like protein 3


Mass: 21639.145 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 109-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP8L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GJ75
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M MES6.7,1.95M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 29427 / Num. obs: 29415 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4M

3f4m


Resolution: 2.3→38.744 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 1490 5.07 %RAMDOM
Rwork0.2398 ---
all0.2409 29427 --
obs0.2409 29415 99.14 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.504 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1937 Å20 Å2-0 Å2
2--8.5487 Å2-0 Å2
3----8.1563 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 45 141 3196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093140
X-RAY DIFFRACTIONf_angle_d1.1374234
X-RAY DIFFRACTIONf_dihedral_angle_d18.3271188
X-RAY DIFFRACTIONf_chiral_restr0.078485
X-RAY DIFFRACTIONf_plane_restr0.005530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2996-2.37380.37591180.3029250298
2.3738-2.45860.34081230.28272497100
2.4586-2.55710.32911400.28022535100
2.5571-2.67340.30551260.26892530100
2.6734-2.81430.28391340.2732543100
2.8143-2.99060.33841350.27712525100
2.9906-3.22140.26511370.26082561100
3.2214-3.54540.24321390.24152531100
3.5454-4.05790.22561360.2119254399
4.0579-5.11070.21931580.1909257299
5.1107-38.74980.26721440.2499258695
Refinement TLS params.Method: refined / Origin x: 3.3279 Å / Origin y: -22.6134 Å / Origin z: -40.9204 Å
111213212223313233
T0.1785 Å20.0089 Å2-0.0016 Å2-0.1446 Å2-0.0355 Å2--0.276 Å2
L1.0425 °2-0.1827 °20.0456 °2-0.7133 °2-0.3464 °2--3.547 °2
S0.0532 Å °-0.1331 Å °0.1338 Å °0.1622 Å °0.0253 Å °-0.0316 Å °0.1477 Å °0.3545 Å °-0.0472 Å °
Refinement TLS groupSelection details: ALL

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