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- PDB-7y8h: Crystal structure of sDscam FNIII1 domain, isoform alpha7 -

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Basic information

Entry
Database: PDB / ID: 7y8h
TitleCrystal structure of sDscam FNIII1 domain, isoform alpha7
ComponentsDown Syndrome Cell Adhesion Molecules
KeywordsCELL ADHESION / cell surface receptor
Function / homology
Function and homology information


anatomical structure morphogenesis / cell-cell adhesion / cell differentiation / 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
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Q. / Yu, Y. / Cheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for the self-recognition of sDSCAM in Chelicerata.
Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q.
History
DepositionJun 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Down Syndrome Cell Adhesion Molecules
B: Down Syndrome Cell Adhesion Molecules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5054
Polymers22,3132
Non-polymers1922
Water1,910106
1
A: Down Syndrome Cell Adhesion Molecules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area5740 Å2
MethodPISA
2
B: Down Syndrome Cell Adhesion Molecules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.977, 43.211, 48.338
Angle α, β, γ (deg.)90.000, 111.287, 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 Down Syndrome Cell Adhesion Molecules


Mass: 11156.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A159W468
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.79 Å3/Da / Density % sol: 31.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG 1,500, 100 mM SPG buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14730 / % possible obs: 99.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.97 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 939 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VA9

1va9


Resolution: 1.8→38.19 Å / SU ML: 0.1884 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2719 732 5.22 %
Rwork0.2229 13286 -
obs0.2255 14018 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 10 106 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691524
X-RAY DIFFRACTIONf_angle_d0.75862085
X-RAY DIFFRACTIONf_chiral_restr0.0513239
X-RAY DIFFRACTIONf_plane_restr0.0055269
X-RAY DIFFRACTIONf_dihedral_angle_d7.64891266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.930.31531220.25492102X-RAY DIFFRACTION75.93
1.93-2.130.28161420.23412751X-RAY DIFFRACTION97.54
2.13-2.440.28661700.23142767X-RAY DIFFRACTION99.36
2.44-3.070.28721450.24282832X-RAY DIFFRACTION99.37
3.07-38.190.24521530.2012834X-RAY DIFFRACTION98.84

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