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- PDB-7y6e: Crystal structure of sDscam FNIII23 domains, isoform Beta2v6 -

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Basic information

Entry
Database: PDB / ID: 7y6e
TitleCrystal structure of sDscam FNIII23 domains, isoform Beta2v6
ComponentsDscam
KeywordsCELL ADHESION / cell surface receptor
Function / homology
Function and homology information


cell-cell adhesion mediator activity / axon guidance / brain development / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.034 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 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dscam
B: Dscam
C: Dscam
D: Dscam
E: Dscam
F: Dscam
G: Dscam


Theoretical massNumber of molelcules
Total (without water)156,5507
Polymers156,5507
Non-polymers00
Water1629
1
A: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dscam


Theoretical massNumber of molelcules
Total (without water)22,3641
Polymers22,3641
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)307.021, 56.219, 94.837
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Dscam


Mass: 22364.230 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Gene: Dscam / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161FW14
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 14% (w/v) PEG 8,000, 100 mM HEPES buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.034→50 Å / Num. obs: 30260 / % possible obs: 98.7 % / Redundancy: 4.7 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.072 / Rrim(I) all: 0.161 / Χ2: 0.926 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.05-3.13.80.76213760.7210.9150.4330.8810.90890.9
3.1-3.1640.76714630.7860.9380.4260.8810.87794.5
3.16-3.224.10.77414480.8040.9440.4220.8860.94497.6
3.22-3.294.30.61515140.8730.9650.3310.7010.98398.8
3.29-3.364.50.56915140.9170.9780.2950.6440.93899.4
3.36-3.434.40.5314850.8990.9730.2740.5990.97199.4
3.43-3.524.60.4415410.9380.9840.2230.4951.00299.3
3.52-3.625.10.37414660.9630.990.1780.4160.95899.7
3.62-3.725.10.32115490.9710.9930.1540.3570.94499.7
3.72-3.8450.25714980.9760.9940.1240.2870.90399.7
3.84-3.9850.2515380.9770.9940.120.2790.98499.7
3.98-4.1450.1815210.9830.9960.0880.2020.95999.9
4.14-4.3350.15515350.9860.9960.0770.1730.95599.7
4.33-4.564.50.12814960.9880.9970.0670.1460.9299.4
4.56-4.8450.11715270.9870.9970.0580.1310.92699.7
4.84-5.215.10.10115560.990.9970.050.1130.90499.9
5.21-5.745.10.09515280.990.9980.0470.1070.81999.7
5.74-6.574.70.09215330.9880.9970.0470.1040.76999.5
6.57-8.274.90.08415650.9860.9960.0420.0940.79799.4
8.27-504.70.09616070.9850.9960.0490.1091.06298.1

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.034→48.847 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 1373 5.29 %
Rwork0.2345 --
obs0.2365 25974 84.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.034→48.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10697 0 0 9 10706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211006
X-RAY DIFFRACTIONf_angle_d0.64415010
X-RAY DIFFRACTIONf_dihedral_angle_d3.046475
X-RAY DIFFRACTIONf_chiral_restr0.0441652
X-RAY DIFFRACTIONf_plane_restr0.0041875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0345-3.14290.3806650.31581298X-RAY DIFFRACTION44
3.1429-3.26870.36151020.28761699X-RAY DIFFRACTION59
3.2687-3.41750.3502980.2831995X-RAY DIFFRACTION69
3.4175-3.59760.3091390.2622310X-RAY DIFFRACTION80
3.5976-3.82290.27731630.26122723X-RAY DIFFRACTION94
3.8229-4.11790.29031560.24862901X-RAY DIFFRACTION100
4.1179-4.53210.28051620.2162877X-RAY DIFFRACTION99
4.5321-5.18730.23211630.19562919X-RAY DIFFRACTION99
5.1873-6.53290.25541630.2252900X-RAY DIFFRACTION99
6.5329-48.8470.24351620.22162979X-RAY DIFFRACTION97

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