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- PDB-5e4i: Crystal structure of mouse CNTN5 Ig1-Ig4 domains -

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Basic information

Entry
Database: PDB / ID: 5e4i
TitleCrystal structure of mouse CNTN5 Ig1-Ig4 domains
ComponentsContactin-5
KeywordsCELL ADHESION / Neural cell adhesion molecule / Immunoglobulin-like domains / Horseshoe-like conformation
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / presynapse assembly / side of membrane / sensory perception of sound / GABA-ergic synapse / presynaptic membrane / cell adhesion
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: 2.6 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) 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 6, 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 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-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0433
Polymers42,6011
Non-polymers4422
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.975, 50.659, 51.015
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Contactin-5 / Neural recognition molecule NB-2


Mass: 42600.988 Da / Num. of mol.: 1 / Fragment: Ig domains 1-4, UNP residues 96-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn5 / Plasmid: pSGHP1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P68500
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1% (v/v) Tacsimate pH 7.0, 20% (w/v) PEG 3350, 50 mM Imidazole-HCl 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: 2.6→50 Å / Num. obs: 13893 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.14 Å2 / Rmerge(I) obs: 0.154 / Χ2: 0.936 / Net I/av σ(I): 11.364 / Net I/σ(I): 4.7 / Num. measured all: 90529
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.693.50.43512820.85390.7
2.69-2.84.60.42913430.90797.5
2.8-2.935.80.35713840.84999.6
2.93-3.086.80.2913870.879100
3.08-3.287.30.24114030.909100
3.28-3.537.40.17613830.937100
3.53-3.887.50.14414261.053100
3.88-4.457.40.12613980.933100
4.45-5.67.40.114260.994100
5.6-507.10.08814610.95199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å36.96 Å
Translation2.6 Å36.96 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JXA

3jxa


Resolution: 2.6→36.963 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1320 9.85 %
Rwork0.1945 12077 -
obs0.2012 13397 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.35 Å2 / Biso mean: 34.2199 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2.6→36.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 28 90 3086
Biso mean--72.69 35.67 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033071
X-RAY DIFFRACTIONf_angle_d0.834171
X-RAY DIFFRACTIONf_chiral_restr0.032463
X-RAY DIFFRACTIONf_plane_restr0.005541
X-RAY DIFFRACTIONf_dihedral_angle_d13.971132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5985-2.70250.41731290.25391101123078
2.7025-2.82540.32761250.26491275140090
2.8254-2.97440.32331440.23661312145695
2.9744-3.16060.34071520.23171353150596
3.1606-3.40450.27891350.21141386152198
3.4045-3.74680.26921500.19571389153999
3.7468-4.28830.24821550.16921413156899
4.2883-5.40010.19771610.14471406156799
5.4001-36.96640.20191690.17381442161199
Refinement TLS params.Method: refined / Origin x: 86.1586 Å / Origin y: 11.9747 Å / Origin z: 12.5035 Å
111213212223313233
T0.2104 Å20.007 Å2-0.0124 Å2-0.196 Å20.0142 Å2--0.1558 Å2
L0.5612 °2-0.0807 °2-0.1408 °2-0.1013 °2-0.011 °2---0.0339 °2
S0.024 Å °0.0308 Å °0.0409 Å °-0.0231 Å °-0.0013 Å °0.0093 Å °-0.0011 Å °0.0032 Å °-0.0246 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA94 - 477
2X-RAY DIFFRACTION1allS1 - 90
3X-RAY DIFFRACTION1allL1 - 2

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