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- PDB-7y54: Crystal structure of sDscam Ig1 domain, isoform alpha1 -

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Basic information

Entry
Database: PDB / ID: 7y54
TitleCrystal structure of sDscam Ig1 domain, isoform alpha1
ComponentsDown Syndrome Cell Adhesion Molecules
KeywordsCELL ADHESION / cell surface receptor
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.787 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 16, 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Down Syndrome Cell Adhesion Molecules


Theoretical massNumber of molelcules
Total (without water)11,0241
Polymers11,0241
Non-polymers00
Water1,45981
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)67.395, 40.728, 41.482
Angle α, β, γ (deg.)90.000, 94.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Down Syndrome Cell Adhesion Molecules


Mass: 11023.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 40% isopropanol, 100 mM Imidazole pH 6.5, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.787→50 Å / Num. obs: 10665 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.96 / Net I/σ(I): 8.6
Reflection shellResolution: 1.787→1.83 Å / Num. unique obs: 508 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZR7

6zr7


Resolution: 1.787→20.686 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 521 5.04 %
Rwork0.1804 9818 -
obs0.1827 10339 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.4 Å2 / Biso mean: 22.4558 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: final / Resolution: 1.787→20.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 0 81 856
Biso mean---30.43 -
Num. residues----100
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7872-1.9670.24651040.1904228290
1.967-2.25130.2381320.1818246498
2.2513-2.83520.22211320.1874252799
2.8352-20.6860.22011530.1741254598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0613-0.8837-0.39761.66530.35491.7327-0.15260.0065-0.45450.06740.10170.08820.2329-0.06660.10380.1623-0.0189-0.00090.09020.00810.1104-1.6602-19.45355.7503
22.04031.1145-0.46573.6515-1.37071.93040.10430.415-0.1491-0.38330.003-0.2879-0.0973-0.0940.05610.17240.07140.02070.1698-0.01540.167415.541-15.107-0.374
31.0518-0.5454-0.27490.8412-0.22361.1351-0.0416-0.23080.07140.11140.09790.00780.01560.0375-0.04760.14960.01930.00560.1484-0.01730.12070.054-11.6959.511
43.4764-2.61750.6552.81830.13742.84140.0171-0.00070.42410.2339-0.260.7981-0.55060.0094-0.00240.374-0.0143-0.07130.4323-0.10930.469515.139-7.8519.154
50.8055-0.405-0.07290.35760.10220.5285-0.0092-0.12870.1874-0.0020.0343-0.14390.03040.0991-0.03060.11540.0157-0.00470.1102-0.00390.14748.5718-10.03926.2517
68.082-2.7194-1.92811.19620.65430.670.0457-0.26670.09650.06160.0447-0.08050.0366-0.0698-0.08040.13520.03-0.01840.18820.02250.0707-7.707-11.44615.025
73.2387-1.0187-0.05141.31510.40880.9783-0.0303-0.19430.10410.18010.1163-0.0680.1488-0.1231-0.0830.13960.03430.0250.18740.05330.1192.996-19.93310.827
85.6021-2.0758-2.77182.3790.43436.0289-0.34480.42760.14950.08710.2503-0.21390.31090.06050.07550.17210.02020.00590.1473-0.00690.184923.988-21.9021.09
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:14)A-1 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:19)A15 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:45)A20 - 45
4X-RAY DIFFRACTION4(chain A and resid 46:49)A46 - 49
5X-RAY DIFFRACTION5(chain A and resid 50:73)A50 - 73
6X-RAY DIFFRACTION6(chain A and resid 74:81)A74 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:92)A82 - 92
8X-RAY DIFFRACTION8(chain A and resid 93:98)A93 - 98

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