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- PDB-4wvr: Crystal structure of Dscam1 Ig7 domain, isoform 5 -

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Basic information

Entry
Database: PDB / ID: 4wvr
TitleCrystal structure of Dscam1 Ig7 domain, isoform 5
ComponentsDown syndrome cell adhesion molecule, isoform AK
KeywordsCELL ADHESION / Ig fold
Function / homology
Function and homology information


mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation ...mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation / regulation of dendrite morphogenesis / regulation of axonogenesis / plasma membrane => GO:0005886 / neuron development / phagocytosis / antigen binding / axon guidance / cell adhesion / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / identical protein binding
Similarity search - Function
Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Basigin-like / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Basigin-like / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Down syndrome cell adhesion molecule 1, isoform G / Down syndrome cell adhesion molecule 1, isoform AK
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsChen, Q. / Yu, Y. / Li, S. / 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
DepositionNov 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Down syndrome cell adhesion molecule, isoform AK
B: Down syndrome cell adhesion molecule, isoform AK
C: Down syndrome cell adhesion molecule, isoform AK
D: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)42,8324
Polymers42,8324
Non-polymers00
Water5,332296
1
A: Down syndrome cell adhesion molecule, isoform AK
D: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)21,4162
Polymers21,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area9850 Å2
MethodPISA
2
B: Down syndrome cell adhesion molecule, isoform AK
C: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)21,4162
Polymers21,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.964, 73.964, 67.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Down syndrome cell adhesion molecule, isoform AK / Dscam1 Ig7 domain / isoform 5


Mass: 10708.091 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: Q0E9K5, UniProt: Q0E9H6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Calcium chloride dihydrate, 30%(w/v) polyethylene glycol monomethyl ether 550, 0.1M Bis-Tris PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2014
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 30014 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 17.7

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Processing

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

3dmk


Resolution: 1.948→28.912 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1488 4.96 %
Rwork0.1822 --
obs0.1842 29981 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→28.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 0 296 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042995
X-RAY DIFFRACTIONf_angle_d0.8694067
X-RAY DIFFRACTIONf_dihedral_angle_d12.7381103
X-RAY DIFFRACTIONf_chiral_restr0.029483
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9484-2.01130.25931420.23142525X-RAY DIFFRACTION98
2.0113-2.08320.2591420.22322615X-RAY DIFFRACTION100
2.0832-2.16660.29141260.20412621X-RAY DIFFRACTION100
2.1666-2.26510.26031450.20382562X-RAY DIFFRACTION100
2.2651-2.38450.24961280.19412621X-RAY DIFFRACTION100
2.3845-2.53380.2471460.20252553X-RAY DIFFRACTION100
2.5338-2.72930.25771330.20922624X-RAY DIFFRACTION100
2.7293-3.00370.27751310.20212587X-RAY DIFFRACTION100
3.0037-3.43780.17561380.18282581X-RAY DIFFRACTION100
3.4378-4.32890.18231350.15292608X-RAY DIFFRACTION100
4.3289-28.91540.20571220.15622596X-RAY DIFFRACTION100

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