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- PDB-5e4q: Crystal structure of mouse CNTN3 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 5e4q
TitleCrystal structure of mouse CNTN3 FN1-FN3 domains
ComponentsContactin-3
KeywordsCELL ADHESION / Neural cell adhesion molecule / 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: 2.822 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

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Assembly

Deposited unit
A: Contactin-3


Theoretical massNumber of molelcules
Total (without water)32,1381
Polymers32,1381
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)185.101, 39.028, 52.408
Angle α, β, γ (deg.)90.000, 96.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32138.453 Da / Num. of mol.: 1 / Fragment: FN domains 1-3, UNP residues 604-900
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn3, Pang, Pcs / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07409
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% (w/v) PEG 1500, 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: Dec 14, 2011
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: 2.8→50 Å / Num. obs: 8976 / % possible obs: 97.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.139 / Χ2: 0.997 / Net I/av σ(I): 15.027 / Net I/σ(I): 6.8 / Num. measured all: 80012
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.95.80.3778180.94690
2.9-3.027.10.3368720.95696.2
3.02-3.158.20.3038691.03697.5
3.15-3.329.10.2458970.96598.8
3.32-3.539.60.2099101.01699
3.53-3.89.90.1778981.04199.1
3.8-4.189.90.1559130.98499.2
4.18-4.799.90.1199260.98199.4
4.79-6.03100.1029180.96999.4
6.03-509.40.079551.0498

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.82 Å45.94 Å
Translation2.82 Å45.94 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: 2.822→47.804 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 448 5 %
Rwork0.1838 8505 -
obs0.187 8953 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.36 Å2 / Biso mean: 56.9949 Å2 / Biso min: 18.55 Å2
Refinement stepCycle: final / Resolution: 2.822→47.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 0 25 2135
Biso mean---38.85 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012164
X-RAY DIFFRACTIONf_angle_d1.2182956
X-RAY DIFFRACTIONf_chiral_restr0.047331
X-RAY DIFFRACTIONf_plane_restr0.006380
X-RAY DIFFRACTIONf_dihedral_angle_d14.241760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8216-3.22980.3111420.2232693283593
3.2298-4.06890.25811510.18652876302799
4.0689-47.81080.21091550.16862936309198
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)
15.9767-0.3912-5.59125.36470.26958.98230.29210.06240.2958-0.5589-0.1453-1.261-0.29171.6485-0.16060.4904-0.00830.1030.91990.00710.5884-15.29937.337-3.9362
27.12041.5985-5.37244.8687-2.22317.08080.1966-0.18250.45330.1997-0.04060.0969-0.53840.2165-0.19610.3182-0.0148-0.03560.1719-0.0250.258-40.84983.183122.7342
39.7761-0.29437.0393.93350.30755.29960.3609-0.0694-0.6660.15050.1612-0.31430.53760.237-0.5590.4206-0.00090.06680.32330.00340.3132-35.8032-10.317458.4318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 604:697))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 698:800))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 801:900))A0

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