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- PDB-5lc2: Xray structure of human FAM3C ILEI monomer -

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Basic information

Entry
Database: PDB / ID: 5lc2
TitleXray structure of human FAM3C ILEI monomer
ComponentsProtein FAM3C
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


platelet dense granule lumen / cytokine activity / Platelet degranulation / carbohydrate binding / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
FAM3C (ILEI) domain / FAM3 family / ILEI/PANDER domain / Interleukin-like EMT inducer / GG-type lectin domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJohansson, P. / Jansson, A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The interleukin-like epithelial-mesenchymal transition inducer ILEI exhibits a non-interleukin-like fold and is active as a domain-swapped dimer.
Authors: Jansson, A.M. / Csiszar, A. / Maier, J. / Nystrom, A.C. / Ax, E. / Johansson, P. / Schiavone, L.H.
History
DepositionJun 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 10, 2024Group: 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FAM3C
B: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)45,3262
Polymers45,3262
Non-polymers00
Water8,053447
1
A: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)22,6631
Polymers22,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)22,6631
Polymers22,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.650, 110.650, 30.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protein FAM3C / Interleukin-like EMT inducer


Mass: 22662.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM3C, ILEI, GS3786 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q92520
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% PEG monomer ether 550, 100 mM MES pH 6.5, 10mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.59→39.1 Å / Num. obs: 46062 / % possible obs: 91.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.94 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOP

2yop


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1673 4.8 %RANDOM
Rwork0.168 ---
obs0.17 34883 99.8 %-
Displacement parametersBiso mean: 27.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.0549 Å20 Å20 Å2
2---0.0549 Å20 Å2
3---0.1097 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 0 447 3039
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012641HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d927SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2641HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion17.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion337SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3346SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.225 150 5.12 %
Rwork0.18 2782 -
all0.182 2932 -
obs--98.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9041-0.15940.3390.5633-0.08221.19390.0397-0.0061-0.15390.1194-0.0092-0.29130.40160.7637-0.03060.17760.2875-0.07230.53410.01380.2291-8.904724.3041.818
21.05560.00560.05740.37990.1710.7980.00130.2510.2778-0.1178-0.10990.295-0.4171-0.62270.10860.16710.3415-0.06780.52750.01480.2886-47.78830.5675-12.7463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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