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- PDB-5xx0: Crystal structure of the four N-terminal immunoglogulin domains o... -

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Basic information

Entry
Database: PDB / ID: 5xx0
TitleCrystal structure of the four N-terminal immunoglogulin domains of Sidekick-2 protein
ComponentsProtein sidekick-2
KeywordsCELL ADHESION / cell-cell adhesion
Function / homology
Function and homology information


SDK interactions / camera-type eye photoreceptor cell differentiation / retina layer formation / homophilic cell adhesion via plasma membrane adhesion molecules / synapse assembly / synapse / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDong, Y. / Tang, H. / He, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Architecture of cell-cell adhesion mediated by sidekicks.
Authors: Tang, H. / Chang, H. / Dong, Y. / Guo, L. / Shi, X. / Wu, Y. / Huang, Y. / He, Y.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein sidekick-2
B: Protein sidekick-2


Theoretical massNumber of molelcules
Total (without water)89,6342
Polymers89,6342
Non-polymers00
Water1,802100
1
A: Protein sidekick-2


Theoretical massNumber of molelcules
Total (without water)44,8171
Polymers44,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein sidekick-2


Theoretical massNumber of molelcules
Total (without water)44,8171
Polymers44,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.356, 86.801, 108.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein sidekick-2


Mass: 44817.137 Da / Num. of mol.: 2 / Fragment: UNP residues 1-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk2, Kiaa1514
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q6V4S5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, 0.1M Bis-Tris, pH5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 30490 / % possible obs: 97.79 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.21
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2890 / % possible all: 93.56

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
DENZOdata reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XWX

5xwx


Resolution: 2.4→28.801 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 2012 6.6 %
Rwork0.2278 --
obs0.2314 30490 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 0 100 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045907
X-RAY DIFFRACTIONf_angle_d0.8458031
X-RAY DIFFRACTIONf_dihedral_angle_d13.5952210
X-RAY DIFFRACTIONf_chiral_restr0.032909
X-RAY DIFFRACTIONf_plane_restr0.0041044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3975-2.45740.34181270.35441887X-RAY DIFFRACTION92
2.4574-2.52390.37171520.33951995X-RAY DIFFRACTION97
2.5239-2.59810.3541390.31771960X-RAY DIFFRACTION96
2.5981-2.68190.38171280.29811993X-RAY DIFFRACTION97
2.6819-2.77770.34971520.28262018X-RAY DIFFRACTION98
2.7777-2.88880.30121370.26992026X-RAY DIFFRACTION99
2.8888-3.02010.29441390.26922035X-RAY DIFFRACTION99
3.0201-3.17910.3481510.27072055X-RAY DIFFRACTION99
3.1791-3.3780.31021510.26432021X-RAY DIFFRACTION99
3.378-3.63840.29421400.23212073X-RAY DIFFRACTION99
3.6384-4.00370.28651500.20452073X-RAY DIFFRACTION100
4.0037-4.5810.24051470.17562076X-RAY DIFFRACTION98
4.581-5.7640.24071470.17932087X-RAY DIFFRACTION99
5.764-28.80350.24761520.20992179X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 180.0905 Å / Origin y: 110.1279 Å / Origin z: 26.2561 Å
111213212223313233
T0.3868 Å20.0638 Å20.0034 Å2-0.2832 Å2-0.0094 Å2--0.3372 Å2
L1.1523 °20.3385 °2-0.2827 °2-0.6868 °20.0124 °2--1.0698 °2
S-0.0512 Å °-0.1793 Å °-0.0418 Å °0.1099 Å °0.0784 Å °-0.051 Å °0.0641 Å °0.2201 Å °-0.0362 Å °
Refinement TLS groupSelection details: all

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