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- PDB-3f4m: Crystal structure of TIPE2 -

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Basic information

Entry
Database: PDB / ID: 3f4m
TitleCrystal structure of TIPE2
ComponentsTumor necrosis factor, alpha-induced protein 8-like protein 2
KeywordsIMMUNE SYSTEM / TIPE2 / immune homeostasis / TNFAIP8
Function / homology
Function and homology information


PI Metabolism / negative regulation of T cell activation / T cell activation / negative regulation of inflammatory response / regulation of apoptotic process / lysosome / innate immune response / nucleus / 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 / Tumor necrosis factor alpha-induced protein 8-like / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.696 Å
AuthorsZhang, X. / Wang, J. / Shi, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Crystal structure of TIPE2 provides insights into immune homeostasis
Authors: Zhang, X. / Wang, J. / Fan, C. / Li, H. / Sun, H. / Gong, S. / Chen, Y.H. / Shi, Y.
History
DepositionNov 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1542
Polymers18,1191
Non-polymers351
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.815, 91.815, 67.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-231-

HOH

31A-234-

HOH

41A-249-

HOH

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Components

#1: Protein Tumor necrosis factor, alpha-induced protein 8-like protein 2 / TIPE2 / Inflammation factor 20


Mass: 18118.830 Da / Num. of mol.: 1 / Fragment: residues 24-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP8L2 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P589
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 13% PEGMME2000, 0.23M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11.5
SYNCHROTRONSPring-8 BL41XU21
ROTATING ANODEBRUKER AXS MICROSTAR-H31.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 28, 2008
ADSC QUANTUM 2102CCDMay 28, 2008
Bruker Platinum 1353CCDFeb 10, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
3GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.51
211
31.54181
ReflectionResolution: 1.696→30 Å / Num. all: 19263 / Num. obs: 19032 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 28.02 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.696→1.76 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1872 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.696→25.829 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.847 / SU ML: 0.23 / σ(F): 1.33 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 972 5.13 %RANDOM
Rwork0.1874 ---
obs0.1901 18952 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.29 Å2 / ksol: 0.432 e/Å3
Displacement parametersBiso max: 76.01 Å2 / Biso mean: 35.154 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.202 Å2-0 Å20 Å2
2---0.202 Å2-0 Å2
3---0.403 Å2
Refinement stepCycle: LAST / Resolution: 1.696→25.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 1 99 1328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041253
X-RAY DIFFRACTIONf_angle_d0.7261694
X-RAY DIFFRACTIONf_chiral_restr0.047194
X-RAY DIFFRACTIONf_plane_restr0.003219
X-RAY DIFFRACTIONf_dihedral_angle_d12.949468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6959-1.78530.26491400.1515253099
1.7853-1.89710.28121430.15032524100
1.8971-2.04360.22661240.1544255999
2.0436-2.24910.23351480.14622563100
2.2491-2.57430.25031450.1535255999
2.5743-3.24240.22191470.18342614100
3.2424-25.8320.24731250.2167263194

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