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- PDB-5i99: Crystal structure of mouse CNTN3 Ig5-Fn2 domains -

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Basic information

Entry
Database: PDB / ID: 5i99
TitleCrystal structure of mouse CNTN3 Ig5-Fn2 domains
ComponentsContactin-3
KeywordsCELL ADHESION / Neural cell adhesion molecule / Immunoglobulin-like domains / Fibronectin type III domains
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell adhesion / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNikolaienko, R.M. / Bouyain, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088806 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.
Authors: Nikolaienko, R.M. / Hammel, M. / Dubreuil, V. / Zalmai, R. / Hall, D.R. / Mehzabeen, N. / Karuppan, S.J. / Harroch, S. / Stella, S.L. / Bouyain, S.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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: Contactin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2212
Polymers43,1281
Non-polymers921
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.227, 76.932, 115.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Contactin-3 / Brain-derived immunoglobulin superfamily protein 1 / BIG-1 / Plasmacytoma-associated neuronal glycoprotein


Mass: 43128.445 Da / Num. of mol.: 1 / Fragment: Ig domains 1-4, UNP residues 406-801
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn3, Pang, Pcs / Plasmid: pET32HP / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: Q07409
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.01 Å3/Da / Density % sol: 59.1 % / Mosaicity: 0.565 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 7.5% (w/v) PEG 8000, 50 mM Imidazole-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20578 / % possible obs: 98.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.44 Å2 / Rmerge(I) obs: 0.165 / Χ2: 0.98 / Net I/av σ(I): 14.875 / Net I/σ(I): 5.9 / Num. measured all: 244693
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.497.90.548187.5
2.49-2.599.30.503195.4
2.59-2.711.20.45199.2
2.7-2.8512.80.3751100
2.85-3.0213.40.2811100
3.02-3.2613.40.2071100
3.26-3.58130.1621100
3.58-4.112.20.1361100
4.1-5.1712.30.111199.9
5.17-5012.50.091199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å43.1 Å
Translation2.4 Å43.1 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.2phasing
PHENIX1.10.1refinement
PDB_EXTRACT3.2data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EV2, 5E4Q

1ev2

5e4q


Resolution: 2.4→43.095 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.84
RfactorNum. reflection% reflection
Rfree0.2531 990 5 %
Rwork0.2028 --
obs0.2053 19803 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.26 Å2 / Biso mean: 41.1634 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 2.4→43.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 6 152 3190
Biso mean--62.86 36.87 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083112
X-RAY DIFFRACTIONf_angle_d0.9424239
X-RAY DIFFRACTIONf_chiral_restr0.059475
X-RAY DIFFRACTIONf_plane_restr0.006554
X-RAY DIFFRACTIONf_dihedral_angle_d11.0591865
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3974-2.52380.29911160.27352111222775
2.5238-2.68190.34361310.27652555268691
2.6819-2.8890.32461340.26162693282795
2.889-3.17960.24921480.23632764291298
3.1796-3.63950.28351510.21332819297099
3.6395-4.58460.25151510.17482865301699
4.5846-43.1020.17781590.14830063165100
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)
17.8352-3.4724-4.73795.67823.85036.5231-0.1720.8104-0.75750.1702-0.45120.8701-0.1408-0.81140.54170.32750.0844-0.08910.4481-0.06760.711949.7481-29.238238.4591
24.1224-1.4511-0.91748.1242-0.42393.2852-0.09670.0455-0.3184-0.02680.1309-0.48830.31580.4189-0.05580.18250.015-0.01180.2241-0.06060.213737.09069.60443.7425
32.9665-2.70210.45473.9237-3.40982.46470.0271-0.14320.23530.2504-0.1586-0.0581-0.09510.19240.12320.22320.0124-0.01310.2151-0.02610.284716.163746.53638.2803
40.66310.42480.05416.29064.45536.38360.0653-0.0108-0.12980.2165-0.18620.10750.4096-0.1480.07150.15170.02090.02990.17290.02520.293315.753685.603749.8188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 404:495))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 496:593))A496 - 593
3X-RAY DIFFRACTION3chain 'A' and ((resseq 594:695))A594 - 695
4X-RAY DIFFRACTION4chain 'A' and ((resseq 696:797))A696 - 797

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