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- PDB-5e55: Crystal structure of mouse CNTN6 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 5.0E+55
TitleCrystal structure of mouse CNTN6 FN1-FN3 domains
ComponentsContactin-6
KeywordsCELL ADHESION / Neural cell adhesion molecule / Fibronectin type III domains
Function / homology
Function and homology information


positive regulation of Notch signaling pathway / parallel fiber to Purkinje cell synapse / side of membrane / Notch signaling pathway / presynapse / presynaptic 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: 2.702 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-6
B: Contactin-6


Theoretical massNumber of molelcules
Total (without water)66,5502
Polymers66,5502
Non-polymers00
Water77543
1
A: Contactin-6


Theoretical massNumber of molelcules
Total (without water)33,2751
Polymers33,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Contactin-6


Theoretical massNumber of molelcules
Total (without water)33,2751
Polymers33,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.744, 90.847, 99.349
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-6 / Neural recognition molecule NB-3 / mNB-3


Mass: 33275.133 Da / Num. of mol.: 2 / Fragment: FN domains 1-3, UNP residues 597-900
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn6 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JMB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300 mM Na-Malonate pH 7.0, 20% (w/v) PEG 3350, 50 mM Na-Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2013
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: 2.7→50 Å / Num. obs: 21656 / % possible obs: 97.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 40.34 Å2 / Rmerge(I) obs: 0.155 / Χ2: 1.002 / Net I/av σ(I): 8.433 / Net I/σ(I): 8.4 / Num. measured all: 160904
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.84.80.51520060.92292.5
2.8-2.915.50.44121160.93797.2
2.91-3.046.70.40521221.05798.7
3.04-3.27.60.32721771.00598.6
3.2-3.47.90.23121550.93799.3
3.4-3.668.20.19821741.04399
3.66-4.038.40.17721731.08299.1
4.03-4.628.40.10922080.96199.4
4.62-5.818.30.08222390.96399.5
5.81-508.10.07422861.05496

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å43.37 Å
Translation2.7 Å43.37 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Coot0.8.1model building
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4S

5e4s


Resolution: 2.702→43.372 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1075 4.98 %
Rwork0.1998 20502 -
obs0.2019 21577 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 42.7963 Å2 / Biso min: 14.56 Å2
Refinement stepCycle: final / Resolution: 2.702→43.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 0 43 4715
Biso mean---34.92 -
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044787
X-RAY DIFFRACTIONf_angle_d0.9176539
X-RAY DIFFRACTIONf_chiral_restr0.035732
X-RAY DIFFRACTIONf_plane_restr0.005853
X-RAY DIFFRACTIONf_dihedral_angle_d14.3761736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7019-2.82490.34161210.31012334245591
2.8249-2.97380.36091360.27192547268398
2.9738-3.160.32551270.25852539266698
3.16-3.40390.26191390.21912578271799
3.4039-3.74630.2551340.20472567270199
3.7463-4.2880.20631340.18812604273899
4.288-5.40080.18121430.14452636277999
5.4008-43.37760.19981410.16822697283897
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)
17.65260.3084-0.04456.05281.22276.4506-0.44240.65730.10170.5280.59250.20510.26360.0364-0.16320.34050.00050.01320.40670.11460.347173.325243.654792.8461
28.15852.39350.8024.4937-0.97592.1154-0.0581-0.2054-0.7411-0.1636-0.1839-0.84140.13950.24180.21150.2985-0.00620.05350.24450.08090.383739.815759.99178.333
32.70751.16670.66692.6383-0.74019.15410.1626-0.3729-0.19330.2641-0.01540.08940.5914-0.8752-0.15170.2145-0.06760.00290.4011-0.02790.21312.813742.750690.4781
46.18573.1542-1.12025.2035-1.54974.4639-0.16790.15330.1874-0.1590.03910.2199-0.2433-0.08440.12540.26410.0559-0.03620.13870.02660.20575.200253.360966.1747
58.3151-0.4244-1.38420.7042-0.5551.65220.10470.14240.03580.0389-0.0921-0.1046-0.1-0.0805-0.01030.25270.0335-0.02980.1492-0.01450.207641.716832.68774.9901
63.5327-1.37132.46622.393-1.95546.8150.11580.4136-0.1141-0.1470.06480.0726-0.1273-0.0222-0.14570.1765-0.04310.0080.3211-0.05170.192811.809746.448660.0757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 596:696))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 697:799))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 800:899))A0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 594:696))B0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 697:799))B0
6X-RAY DIFFRACTION6chain 'B' and ((resseq 800:900))B0

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