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- PDB-7ltw: Crystal structure of the mouse Kirrel2 D1 homodimer -

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Basic information

Entry
Database: PDB / ID: 7ltw
TitleCrystal structure of the mouse Kirrel2 D1 homodimer
ComponentsKin of IRRE-like protein 2
KeywordsCELL ADHESION / Immunoglobulin superfamily / Cell surface receptor / Nervous system
Function / homology
Function and homology information


Nephrin family interactions / slit diaphragm / plasma membrane => GO:0005886 / cell adhesion molecule binding / negative regulation of protein phosphorylation / cell-cell adhesion / cell-cell junction / identical protein binding / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Kin of IRRE-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRoman, C.A. / Pak, J.S. / Wang, J. / Ozkan, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RF1MH114102 United States
CitationJournal: Cell Rep / Year: 2021
Title: Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors.
Authors: Wang, J. / Vaddadi, N. / Pak, J.S. / Park, Y. / Quilez, S. / Roman, C.A. / Dumontier, E. / Thornton, J.W. / Cloutier, J.F. / Ozkan, E.
History
DepositionFeb 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Kin of IRRE-like protein 2
B: Kin of IRRE-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9734
Polymers23,9272
Non-polymers462
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-23 kcal/mol
Surface area10440 Å2
Unit cell
Length a, b, c (Å)109.137, 48.444, 44.102
Angle α, β, γ (deg.)90.000, 107.006, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Kin of IRRE-like protein 2 / Kin of irregular chiasm-like protein 2


Mass: 11963.345 Da / Num. of mol.: 2 / Fragment: Domain 1, residues 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kirrel2, Neph3 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7TSU7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Potassium/Sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2015
RadiationMonochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19361 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 14.68 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Rsym value: 0.056 / Net I/av σ(I): 21.9 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 715 / CC1/2: 0.945 / CC star: 0.986 / Rpim(I) all: 0.124 / Rrim(I) all: 0.214 / Rsym value: 0.173 / % possible all: 69.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Cootmodel building
PHASER2.6.0phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OFI

4ofi


Resolution: 1.8→32.49 Å / SU ML: 0.1611 / Cross valid method: FREE R-VALUE / Phase error: 17.8417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 971 5.02 %random
Rwork0.1549 18390 --
obs0.1562 19361 94.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 2 337 1953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361681
X-RAY DIFFRACTIONf_angle_d0.6322288
X-RAY DIFFRACTIONf_chiral_restr0.0462234
X-RAY DIFFRACTIONf_plane_restr0.0042307
X-RAY DIFFRACTIONf_dihedral_angle_d12.8399622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.90.25181190.1952161X-RAY DIFFRACTION78.51
1.9-2.010.20541390.16522677X-RAY DIFFRACTION96.17
2.02-2.170.18081400.14972651X-RAY DIFFRACTION96.91
2.17-2.390.19051450.16362715X-RAY DIFFRACTION96.85
2.39-2.730.20131380.1642693X-RAY DIFFRACTION96.82
2.73-3.440.18661440.15862713X-RAY DIFFRACTION96.91
3.44-32.490.14081460.13672780X-RAY DIFFRACTION97.31

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