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- PDB-7y73: Crystal structure of sDscam Ig1 domain, isoform beta3v7 -

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Basic information

Entry
Database: PDB / ID: 7y73
TitleCrystal structure of sDscam Ig1 domain, isoform beta3v7
ComponentsDown Syndrome Cell Adhesion Molecules
KeywordsCELL ADHESION / cell surface recptor
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 21, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)22,0553
Polymers21,9632
Non-polymers921
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.649, 40.950, 54.231
Angle α, β, γ (deg.)90.000, 100.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Down Syndrome Cell Adhesion Molecules


Mass: 10981.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M TRIS pH8.5, 20%(w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 39096 / % possible obs: 98.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 12.48 Å2 / CC1/2: 0.98 / Net I/σ(I): 17.9
Reflection shellResolution: 1.32→1.36 Å / Num. unique obs: 2249 / CC1/2: 0.87

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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: 6ZR7

6zr7


Resolution: 1.32→39.03 Å / SU ML: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.8885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 1752 4.94 %
Rwork0.1884 33739 -
obs0.19 35491 88.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.52 Å2
Refinement stepCycle: LAST / Resolution: 1.32→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 6 238 1760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531583
X-RAY DIFFRACTIONf_angle_d0.78562153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.3028870.24651657X-RAY DIFFRACTION57.16
1.36-1.40.29451240.24972200X-RAY DIFFRACTION75.48
1.4-1.440.27151300.22762522X-RAY DIFFRACTION86.78
1.44-1.490.24211090.22182614X-RAY DIFFRACTION88.18
1.49-1.550.26961320.20232762X-RAY DIFFRACTION93.9
1.55-1.620.24361390.19122836X-RAY DIFFRACTION95.75
1.62-1.710.21771440.17422787X-RAY DIFFRACTION95.07
1.71-1.820.23811390.18472804X-RAY DIFFRACTION95
1.82-1.960.19881480.1752672X-RAY DIFFRACTION91.09
1.96-2.150.17141350.1632759X-RAY DIFFRACTION93.2
2.15-2.470.22571770.17892745X-RAY DIFFRACTION93.35
2.47-3.110.23561490.19082672X-RAY DIFFRACTION90.59
3.11-39.030.20491390.19012709X-RAY DIFFRACTION88.83

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