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- PDB-7y5r: Crystal structure of sDscam FNIII2 domain, isoform alpha7 -

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Basic information

Entry
Database: PDB / ID: 7y5r
TitleCrystal structure of sDscam FNIII2 domain, isoform alpha7
ComponentsDown Syndrome Cell Adhesion Molecules
KeywordsCELL ADHESION / cell surface receptor
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.562 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 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7544
Polymers11,4781
Non-polymers2763
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-0 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.853, 53.280, 60.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Down Syndrome Cell Adhesion Molecules


Mass: 11477.840 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 13917 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.051 / Rrim(I) all: 0.181 / Χ2: 0.985 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.56-1.69.70.4059170.9470.1340.4271.235
1.6-1.6410.90.48880.9460.1260.421.248
1.64-1.6811.20.3729280.9540.1140.3891.22
1.68-1.7311.40.3548840.9650.1080.371.235

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VA9

1va9


Resolution: 1.562→26.64 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1588 707 5.18 %
Rwork0.1387 12943 -
obs0.1398 13650 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.44 Å2 / Biso mean: 15.9402 Å2 / Biso min: 5.2 Å2
Refinement stepCycle: final / Resolution: 1.562→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 41 162 1015
Biso mean--38.4 26.79 -
Num. residues----105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.562-1.68230.181260.156249296
1.6823-1.85150.17351440.1365250798
1.8515-2.11930.14211520.1247257399

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