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- PDB-5e4s: Crystal structure of mouse CNTN4 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 5e4s
TitleCrystal structure of mouse CNTN4 FN1-FN3 domains
ComponentsContactin-4
KeywordsCELL ADHESION / Neural cell adhesion molecule / Fibronectin type III domains
Function / homology
Function and homology information


negative regulation of neuron differentiation / side of membrane / brain development / neuron projection development / nervous system development / cell adhesion / extracellular region / 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 ...: / 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: 2.5 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
DepositionOct 7, 2015Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-4


Theoretical massNumber of molelcules
Total (without water)33,1661
Polymers33,1661
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.792, 144.298, 55.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-955-

HOH

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Components

#1: Protein Contactin-4 / Brain-derived immunoglobulin superfamily protein 2 / BIG-2


Mass: 33166.129 Da / Num. of mol.: 1 / Fragment: FN domains 1-3, UNP residues 596-898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn4, Kiaa3024 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q69Z26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM (NH4)2SO4, 50 mM Tris-HCl pH 8.5, 10% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2011
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13387 / % possible obs: 98.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 52.36 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.913 / Net I/av σ(I): 20.733 / Net I/σ(I): 7.8 / Num. measured all: 81192
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.594.20.4611430.78387.4
2.59-2.695.40.40412960.82596.1
2.69-2.826.10.29613360.84599.6
2.82-2.966.40.213400.839100
2.96-3.156.50.1413380.849100
3.15-3.396.50.0913570.943100
3.39-3.736.40.07313570.95100
3.73-4.276.40.07213830.888100
4.27-5.386.30.08613781.086100
5.38-5060.03714591.03999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å28.71 Å
Translation2.5 Å28.71 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
Coot0.8.1model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7L

5e7l


Resolution: 2.5→28.706 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 668 5 %
Rwork0.1904 12701 -
obs0.1937 13369 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 61.5482 Å2 / Biso min: 32.97 Å2
Refinement stepCycle: final / Resolution: 2.5→28.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 0 69 2394
Biso mean---53.48 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092387
X-RAY DIFFRACTIONf_angle_d1.1163257
X-RAY DIFFRACTIONf_chiral_restr0.043361
X-RAY DIFFRACTIONf_plane_restr0.006424
X-RAY DIFFRACTIONf_dihedral_angle_d12.693870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.68150.35841180.26182238235688
2.6815-2.95110.35481340.268125602694100
2.9511-3.37760.29021360.232725722708100
3.3776-4.25320.26721380.18826212759100
4.2532-28.70740.1921420.144927102852100
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)
13.3678-0.6221-0.48843.657-0.3553.09220.0260.37360.057-0.4707-0.15320.3534-0.6193-0.5090.17910.50320.0762-0.18110.422-0.11590.553960.148859.4763-6.0319
24.22660.2636-0.00272.1004-0.5531.6449-0.1065-0.4674-0.0420.19530.1260.1246-0.0347-0.1504-0.02080.26520.01110.05350.34310.00880.349683.455341.804820.445
34.74241.27371.84054.2356-0.33582.23960.0674-0.21890.31310.7316-0.15760.035-0.6779-0.29110.04720.71360.0681-0.04150.4974-0.01360.3106109.114263.747539.1021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 596:698))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 699:799))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 800:898))A0

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