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- PDB-5lc4: Xray structure of mouse FAM3C ILEI dimer -

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Basic information

Entry
Database: PDB / ID: 5lc4
TitleXray structure of mouse FAM3C ILEI dimer
ComponentsProtein FAM3C
KeywordsSIGNALING PROTEIN
Function / homologyFAM3C (ILEI) domain / FAM3 family / ILEI/PANDER domain / Interleukin-like EMT inducer / Platelet degranulation / cytoplasmic vesicle / Golgi apparatus / extracellular space / Protein FAM3C
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.3Jan 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

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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
C: Protein FAM3C
D: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)90,8284
Polymers90,8284
Non-polymers00
Water7,620423
1
A: Protein FAM3C
D: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)45,4142
Polymers45,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-32 kcal/mol
Surface area16780 Å2
MethodPISA
2
B: Protein FAM3C
C: Protein FAM3C


Theoretical massNumber of molelcules
Total (without water)45,4142
Polymers45,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-32 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.750, 118.450, 85.420
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22707.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fam3c, D6Wsu176e, Ilei / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q91VU0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ILEI dimer 10 mg/mL + 3.3 M (NH4)2SO4, 1% MPD, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→48.5 Å / Num. obs: 69589 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.75 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.2
Reflection shellResolution: 1.84→1.89 Å

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Processing

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

2yop


Resolution: 1.84→48.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3465 4.99 %RANDOM
Rwork0.212 ---
obs0.213 69451 97.8 %-
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.6319 Å20 Å2-1.4078 Å2
2--5.3737 Å20 Å2
3----2.7418 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.84→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 0 423 5636
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085320HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017172HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1866SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes137HARMONIC2
X-RAY DIFFRACTIONt_gen_planes762HARMONIC5
X-RAY DIFFRACTIONt_it5320HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion18.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion696SEMIHARMONIC5
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_contact6244SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 231 5.23 %
Rwork0.223 4186 -
all0.224 4417 -
obs--84.16 %
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)
1-0.076-0.3140.30511.4148-0.64350.1936-0.00220.03330.1029-0.165-0.0506-0.12270.0446-0.02250.0527-0.052-0.01480.0354-0.05040.0272-0.0555-1.721310.2291-43.467
20.06480.511-0.20062.1125-0.99990.1858-0.0206-0.1027-0.07750.2476-0.098-0.1764-0.00690.04910.1186-0.04540.00550.0016-0.06440.038-0.082713.175-23.31671.121
3-0.1559-0.34060.49272.0991-0.90140.15590.07560.03820.1052-0.2471-0.0558-0.1138-0.0297-0.0152-0.0199-0.0266-0.00990.1064-0.0880.0245-0.061813.1887-44.50451.9137
40.09560.6424-0.30861.9637-0.5825-0.00960.0366-0.0871-0.10050.2347-0.0818-0.1856-0.0102-0.00520.0452-0.05760.0094-0.0349-0.07820.0364-0.0512-0.566131.3249-44.435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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