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- PDB-7mro: Zebrafish CNTN4 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 7mro
TitleZebrafish CNTN4 FN1-FN3 domains
ComponentsContactin-4
KeywordsCELL ADHESION / Ig superfamily
Function / homology
Function and homology information


cell-cell adhesion mediator activity / axon guidance / brain development / cell-cell adhesion / axon / 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
Similarity search - Domain/homology
Contactin-4 precursor
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBouyain, S. / Karuppan, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R15NS108371-01 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Members of the vertebrate contactin and amyloid precursor protein families interact through a conserved interface.
Authors: Karuppan, S.J. / Vogt, A. / Fischer, Z. / Ladutska, A. / Swiastyn, J. / McGraw, H.F. / Bouyain, S.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,2171
Polymers33,2171
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.700, 56.880, 130.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Contactin-4 / Zgc:153573


Mass: 33217.207 Da / Num. of mol.: 1 / Fragment: FN1-FN3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cntn4, zgc:153573 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08C52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Na-acetate pH 5.5, 30% (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→56.88 Å / Num. obs: 28351 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.037 / Rrim(I) all: 0.136 / Net I/σ(I): 12.7
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 1791 / CC1/2: 0.978 / Rpim(I) all: 0.075 / Rrim(I) all: 0.285 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4S

5e4s


Resolution: 1.87→36.92 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.4875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1999 7.07 %
Rwork0.1742 26275 -
obs0.1772 28274 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.87→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 394 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642389
X-RAY DIFFRACTIONf_angle_d0.84253269
X-RAY DIFFRACTIONf_chiral_restr0.0585363
X-RAY DIFFRACTIONf_plane_restr0.0059423
X-RAY DIFFRACTIONf_dihedral_angle_d13.3423868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.26661380.19171816X-RAY DIFFRACTION99.9
1.92-1.970.23261420.18971856X-RAY DIFFRACTION100
1.97-2.030.21861410.17731864X-RAY DIFFRACTION99.85
2.03-2.090.20271400.17551825X-RAY DIFFRACTION100
2.09-2.170.22431410.17051855X-RAY DIFFRACTION99.95
2.17-2.260.25941420.1841868X-RAY DIFFRACTION99.85
2.26-2.360.19921410.18541855X-RAY DIFFRACTION99.95
2.36-2.480.21641410.18751866X-RAY DIFFRACTION99.9
2.48-2.640.25421420.19561862X-RAY DIFFRACTION99.9
2.64-2.840.27611430.19511875X-RAY DIFFRACTION99.85
2.84-3.130.20291420.18821885X-RAY DIFFRACTION99.9
3.13-3.580.19861450.16521897X-RAY DIFFRACTION100
3.58-4.510.19141470.1531928X-RAY DIFFRACTION100
4.51-36.920.19821540.15622023X-RAY DIFFRACTION99.54
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)
10.781598309081-0.331598944994-0.6238356205381.438199154971.222121032152.716408500230.01086692884450.07402630153150.140978725692-0.2403479750460.0373630835355-0.239666926435-0.2520473675960.0065859687479-0.05182323704590.148089361894-0.01761650206050.01592978119330.074769681390.0002895039803250.15472810530246.311152257525.948019866827.3681141066
22.354833294170.222319227087-0.758804683962.597698262371.31514826475.118753807280.1220695557090.0263354373045-0.06680172317120.180567376208-0.1069593729920.1289659427750.0392735721135-0.232773171032-0.02217640091230.068267255625-0.0029457118738-0.002484948160480.0938426462021-0.02877616282550.11589588309422.824181765333.528240135356.0408958122
32.401743598291.279189230380.1334651675384.615289350341.150052344822.183437056590.0115698184659-0.01838951527950.37564346946-0.106010688069-0.0266960051405-0.0448197424002-0.3249212085490.007040330873170.001960185086530.0997234012060.005517368868080.01979059741010.124693588143-0.009072102434540.13760235156728.836629729461.52921294479.372528082
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 598 through 712 )598 - 7121 - 115
22chain 'A' and (resid 713 through 799 )713 - 799116 - 202
33chain 'A' and (resid 800 through 901 )800 - 901203 - 304

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