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- PDB-7mrq: Chicken CNTN4 FN1-FN3 domains with T751A, V752A, Y781A, E786A mut... -

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Basic information

Entry
Database: PDB / ID: 7mrq
TitleChicken CNTN4 FN1-FN3 domains with T751A, V752A, Y781A, E786A mutations
ComponentsContactin-4
KeywordsCELL ADHESION / Ig superfamily
Function / homology
Function and homology information


axon guidance / cell adhesion / plasma membrane
Similarity search - Function
Basigin-like / 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 ...Basigin-like / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 8, 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)33,3501
Polymers33,3501
Non-polymers00
Water00
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)71.010, 91.460, 124.290
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


Mass: 33350.027 Da / Num. of mol.: 1 / Fragment: FN1-FN3 domains / Mutation: T751A, V752A, Y781A, E786A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: F1P3U6

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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: 6.03 Å3/Da / Density % sol: 79.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4.2M NaCl, 2 (v/v) % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13597 / % possible obs: 95.1 % / Redundancy: 11.3 % / Biso Wilson estimate: 103.76 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.202 / Net I/σ(I): 12
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1014 / CC1/2: 0.846 / Rrim(I) all: 0.812 / % possible all: 71.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4S

5e4s


Resolution: 3.2→46.77 Å / SU ML: 0.4601 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 1350 10.06 %
Rwork0.2209 12065 -
obs0.225 13415 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.56 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 0 0 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552332
X-RAY DIFFRACTIONf_angle_d0.81963192
X-RAY DIFFRACTIONf_chiral_restr0.0551358
X-RAY DIFFRACTIONf_plane_restr0.0068420
X-RAY DIFFRACTIONf_dihedral_angle_d12.469846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.43731130.3511973X-RAY DIFFRACTION80.38
3.31-3.450.40471220.33121098X-RAY DIFFRACTION89.57
3.45-3.60.31911330.29411177X-RAY DIFFRACTION95.97
3.6-3.790.27191360.23991226X-RAY DIFFRACTION99.71
3.79-4.030.26751380.21911235X-RAY DIFFRACTION99.93
4.03-4.340.25971380.21121233X-RAY DIFFRACTION99.93
4.34-4.780.23161390.17611248X-RAY DIFFRACTION99.78
4.78-5.470.19841410.16771265X-RAY DIFFRACTION100
5.47-6.890.24241400.21251260X-RAY DIFFRACTION100
6.89-46.770.26241500.22721350X-RAY DIFFRACTION99.73
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)
18.48842137447-1.601907529942.284969210377.12237894506-1.507406657674.961352263270.8136466545260.204131524719-1.74596894163-0.754598571546-0.02918027642640.2549919139431.85179721120.327761448893-0.7624693211551.979039596160.00356226582333-0.3140452445890.666523602901-0.04752217790691.1446053788622.7165653589-47.81096292324.3052667978
27.75827068099-3.80761395041.850385130099.27629147125-2.77078499796.845233378550.468585623490.06991179789180.4096103147080.622980796754-0.221362465291-0.0387867117807-0.4848470388660.136963993716-0.2908138322161.29453727228-0.1756240388120.02661871855180.6227034629330.001865333392640.6828026801252.83773466502-17.5831364525-15.2744853862
38.178571556784.18229536114-2.135785590164.92351329514-4.625047410929.38979245506-0.0968522073409-0.370306188808-0.679423746743-0.508504319723-0.752532241238-1.306589978870.5033858782930.7530785593520.885341828181.372239409860.196064628130.09846006966860.7122506341240.1692979106640.93379038157111.073013956915.5718709264-40.5642946398
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 697 )598 - 6971 - 100
22chain 'A' and (resid 698 through 799 )698 - 799101 - 202
33chain 'A' and (resid 800 through 900 )800 - 900203 - 297

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