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- PDB-7y95: Crystal structure of sDscam Ig1 domain, isoform beta6v2 -

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Basic information

Entry
Database: PDB / ID: 7y95
TitleCrystal structure of sDscam Ig1 domain, isoform beta6v2
ComponentsDscam
KeywordsCELL ADHESION / cell surface receptor
Function / homology
Function and homology information


axon guidance / cell-cell adhesion / axon / plasma 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: 1.55 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 24, 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 1.2Nov 13, 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: Dscam
B: Dscam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,76612
Polymers21,3982
Non-polymers36810
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-76 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.177, 39.096, 60.873
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dscam


Mass: 10698.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Gene: Dscam / Production host: Escherichia coli (E. coli) / References: UniProt: A0A159W5Q3
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Formate, 20% (w/v) PEG3,350

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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 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 30014 / % possible obs: 99.6 % / Redundancy: 5.7 % / CC1/2: 0.991 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.584.10.60914720.8240.3270.6950.45697.9
1.58-1.614.60.52714250.8490.2670.5930.4499.3
1.61-1.645.30.56314620.8650.2620.6230.44699.6
1.64-1.675.40.49514680.9190.230.5480.43999.8
1.67-1.715.60.4514740.9190.2060.4960.47399.7
1.71-1.755.50.44914620.9230.2060.4960.51199.9
1.75-1.795.50.39714430.9370.1840.4390.47599.9
1.79-1.845.30.34214660.9550.1610.3790.55499.4
1.84-1.895.30.33814690.9490.1590.3750.78799.6
1.89-1.9560.35814810.9390.1540.3911.45599.9
1.95-2.026.20.22414610.980.0960.2440.83799.8
2.02-2.16.30.27414670.7320.1190.31.89699.6
2.1-2.26.30.15314730.9840.0660.1670.88399.6
2.2-2.325.90.21114860.9830.0940.2321.33599.5
2.32-2.465.70.09214600.990.0440.1030.44799.7
2.46-2.656.60.07415030.9970.0310.0810.48599.9
2.65-2.926.50.0614630.9980.0250.0650.64999.6
2.92-3.3460.04214940.9980.0190.0460.55799.7
3.34-4.216.10.04115030.9970.0180.0450.81399.9
4.21-5060.03115470.9960.0130.0342.03599.3

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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: 1.55→19.548 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 901 3 %
Rwork0.1509 29113 -
obs0.1521 30014 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.02 Å2 / Biso mean: 28.4671 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 1.55→19.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 36 241 1778
Biso mean--63.67 37.56 -
Num. residues----198
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.63460.36511480.274477699
1.6346-1.76080.27881490.19084840100
1.7608-1.93780.25761490.16784818100
1.9378-2.21790.18551500.12764820100
2.2179-2.7930.17671510.14524893100
2.793-19.5480.15831540.14264966100

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