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- PDB-7y4x: Crystal structure of sDscam Ig1 domain, isoform alpha7 -

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Basic information

Entry
Database: PDB / ID: 7y4x
TitleCrystal structure of sDscam Ig1 domain, isoform alpha7
ComponentsDown syndrome cell adhesion molecule
KeywordsCELL ADHESION / cell surface receptor
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.952 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 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 molecule
B: Down syndrome cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2194
Polymers21,7772
Non-polymers4422
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-0 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 92.530, 69.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Down syndrome cell adhesion molecule


Mass: 10888.456 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.43 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 25% PEG 3,350, 5% Jeffamine M-600 pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 6793 / % possible obs: 99.9 % / Redundancy: 24.3 % / CC1/2: 0.965 / CC star: 0.991 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.043 / Rrim(I) all: 0.214 / Χ2: 1.006 / Net I/σ(I): 4.5 / Num. measured all: 164824
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-317.41.423290.7410.9230.3451.4620.9799.4
3-3.0618.41.1733280.8470.9580.2781.2071.0499.7
3.06-3.1121.71.0913270.8950.9720.2371.1171.04199.7
3.11-3.1824.61.0533330.9290.9810.2131.0751.074100
3.18-3.2525.80.833180.9330.9820.1650.8461.053100
3.25-3.3225.80.7373360.9510.9870.1460.7521.024100
3.32-3.4126.60.73410.9620.990.1370.7141.034100
3.41-3.525.80.5273230.9760.9940.1040.5381.02100
3.5-3.6260.4213260.980.9950.0840.431.072100
3.6-3.7224.40.3293480.9880.9970.0670.3361.066100
3.72-3.8524.50.2723330.9920.9980.0550.2771.032100
3.85-426.70.2353310.9930.9980.0460.2391.023100
4-4.1926.50.1883410.9950.9990.0370.1920.98100
4.19-4.4125.90.1693360.9950.9990.0340.1720.946100
4.41-4.6825.70.1443410.9960.9990.0290.1470.91100
4.68-5.0423.70.1353420.9960.9990.0270.1380.871100
5.04-5.5526.20.1343420.9940.9980.0260.1370.861100
5.55-6.3525.30.1343580.9970.9990.0270.1360.855100
6.35-8230.1243570.9970.9990.0260.1270.868100
8-5021.60.1624030.9930.9980.0350.1661.38999.8

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6zr7

6zr7


Resolution: 2.952→32.714 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 355 5.33 %
Rwork0.2103 --
obs0.2122 6660 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.952→32.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 28 4 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031572
X-RAY DIFFRACTIONf_angle_d0.7572144
X-RAY DIFFRACTIONf_dihedral_angle_d3.146942
X-RAY DIFFRACTIONf_chiral_restr0.068260
X-RAY DIFFRACTIONf_plane_restr0.005268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9524-3.37920.31151090.25631993X-RAY DIFFRACTION96
3.3792-4.2560.23291160.20992106X-RAY DIFFRACTION100
4.256-32.7140.23121300.19462206X-RAY DIFFRACTION100

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