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- PDB-4x5l: Crystal structure of Dscam1 Ig7 domain, isoform 9 -

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Basic information

Entry
Database: PDB / ID: 4x5l
TitleCrystal structure of Dscam1 Ig7 domain, isoform 9
ComponentsDown syndrome cell adhesion molecule, isoform AM
KeywordsCELL ADHESION / Ig fold
Function / homology
Function and homology information


DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / homophilic cell-cell adhesion / phagocytosis / neuron development / antigen binding / axon guidance / central nervous system development / perikaryon / neuron projection / axon / neuronal cell body / dendrite / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / 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. ...Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / 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
Cell adhesion molecule Dscam1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 Å
AuthorsChen, Q. / Yu, Y. / Li, S.A. / Cheng, L.
CitationJournal: Sci Adv / Year: 2016
Title: Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition
Authors: Li, S.A. / Cheng, L. / Yu, Y. / Chen, Q.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Down syndrome cell adhesion molecule, isoform AM
B: Down syndrome cell adhesion molecule, isoform AM
C: Down syndrome cell adhesion molecule, isoform AM
D: Down syndrome cell adhesion molecule, isoform AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9946
Polymers42,9484
Non-polymers462
Water1,856103
1
A: Down syndrome cell adhesion molecule, isoform AM

A: Down syndrome cell adhesion molecule, isoform AM


Theoretical massNumber of molelcules
Total (without water)21,4742
Polymers21,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-x+3,-y+2,z1
Buried area1790 Å2
ΔGint-11 kcal/mol
Surface area8940 Å2
MethodPISA
2
B: Down syndrome cell adhesion molecule, isoform AM
hetero molecules

B: Down syndrome cell adhesion molecule, isoform AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5204
Polymers21,4742
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z1
Buried area1810 Å2
ΔGint-31 kcal/mol
Surface area9290 Å2
MethodPISA
3
C: Down syndrome cell adhesion molecule, isoform AM

C: Down syndrome cell adhesion molecule, isoform AM


Theoretical massNumber of molelcules
Total (without water)21,4742
Polymers21,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-x+3,-y+2,z1
Buried area1660 Å2
ΔGint-12 kcal/mol
Surface area9250 Å2
MethodPISA
4
D: Down syndrome cell adhesion molecule, isoform AM
hetero molecules

D: Down syndrome cell adhesion molecule, isoform AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5204
Polymers21,4742
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.527, 117.370, 117.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

21D-210-

HOH

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Components

#1: Protein
Down syndrome cell adhesion molecule, isoform AM / Dscam1 Ig7 domain / isoform 9


Mass: 10737.034 Da / Num. of mol.: 4 / Fragment: UNP residues 617-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam1, Dscam, CG17800, Dmel_CG17800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0E9K7
#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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES PH 7.5, 0.7 M sodium phosphate monobasic, 0.7 M potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979104 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979104 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 26120 / % possible obs: 99.5 % / Redundancy: 7.1 % / Net I/σ(I): 21.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DMK

3dmk


Resolution: 2.374→45.527 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2472 1006 3.85 %
Rwork0.2147 --
obs0.2214 26120 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.374→45.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 2 103 2993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032952
X-RAY DIFFRACTIONf_angle_d0.754028
X-RAY DIFFRACTIONf_dihedral_angle_d12.7491060
X-RAY DIFFRACTIONf_chiral_restr0.03472
X-RAY DIFFRACTIONf_plane_restr0.003532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.377-2.50230.38991400.29563522X-RAY DIFFRACTION96
2.5023-2.6590.32951440.27993515X-RAY DIFFRACTION96
2.659-2.86420.35211420.28173572X-RAY DIFFRACTION96
2.8642-3.15230.3541360.26163524X-RAY DIFFRACTION96
3.1523-3.6080.23711430.2173573X-RAY DIFFRACTION96
3.608-4.54410.20921450.17853610X-RAY DIFFRACTION96
4.5441-34.39520.21331540.19573769X-RAY DIFFRACTION95

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