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- PDB-5k6w: Sidekick-1 immunoglobulin domains 1-5 -

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Basic information

Entry
Database: PDB / ID: 5k6w
TitleSidekick-1 immunoglobulin domains 1-5
ComponentsProtein sidekick-1
KeywordsCELL ADHESION / immunoglobulin
Function / homology
Function and homology information


SDK interactions / retina layer formation / regulation of dendritic spine development / cell-cell adhesion mediator activity / homophilic cell adhesion via plasma membrane adhesion molecules / behavioral response to cocaine / synapse assembly / axon guidance / brain development / axon ...SDK interactions / retina layer formation / regulation of dendritic spine development / cell-cell adhesion mediator activity / homophilic cell adhesion via plasma membrane adhesion molecules / behavioral response to cocaine / synapse assembly / axon guidance / brain development / axon / synapse / identical protein binding / 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 / Resolution: 3.5 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Honig, B. / Shapiro, L.
CitationJournal: Elife / Year: 2016
Title: Molecular basis of sidekick-mediated cell-cell adhesion and specificity.
Authors: Goodman, K.M. / Yamagata, M. / Jin, X. / Mannepalli, S. / Katsamba, P.S. / Ahlsen, G. / Sergeeva, A.P. / Honig, B. / Sanes, J.R. / Shapiro, L.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein sidekick-1
B: Protein sidekick-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,90016
Polymers105,7382
Non-polymers3,16214
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-10 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.140, 152.870, 158.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein sidekick-1


Mass: 52869.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GPALA are expression construct derived and would be cleaved in the native protein
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk1 / Production host: Homo sapiens (human) / References: UniProt: Q3UH53

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Sugars , 3 types, 9 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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Non-polymers , 3 types, 11 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 1.4M ammonium sulfate, 0.5M lithium chloride, 10mM yttrium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 19853 / % possible obs: 89.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 62.67 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.9
Reflection shellResolution: 3.5→3.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.9 / % possible all: 79.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.5→36.997 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1027 5.17 %
Rwork0.2018 --
obs0.2044 19853 89.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→36.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 201 6 7109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037279
X-RAY DIFFRACTIONf_angle_d0.61310013
X-RAY DIFFRACTIONf_dihedral_angle_d10.1494310
X-RAY DIFFRACTIONf_chiral_restr0.0431223
X-RAY DIFFRACTIONf_plane_restr0.0041275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.68440.32361320.24522327X-RAY DIFFRACTION79
3.6844-3.9150.26241480.21762432X-RAY DIFFRACTION82
3.915-4.21690.24471400.19312529X-RAY DIFFRACTION86
4.2169-4.64050.23791460.1722715X-RAY DIFFRACTION91
4.6405-5.31030.2311540.17442857X-RAY DIFFRACTION95
5.3103-6.6840.26661510.22072942X-RAY DIFFRACTION97
6.684-36.99940.23271560.21573024X-RAY DIFFRACTION95
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)
11.39572.2594-1.16843.9231-2.32413.31460.0591-0.02790.44470.01470.12750.7454-0.0662-0.0269-0.15060.25490.08010.03610.4860.0750.407513.1681-14.4115-10.0934
22.1409-3.329-1.96125.16524.96645.03990.2494-0.1273-0.06920.2896-0.4607-0.0860.0739-0.32730.29380.27260.0168-0.0060.43650.05930.332927.1496-44.3178-5.6073
33.34642.1864-0.77595.40712.40873.7836-0.02560.1545-0.042-0.21-0.2350.31260.3763-0.21930.2240.42520.0561-0.09430.4095-0.02760.23347.743-56.3867-16.5028
44.03722.3730.44768.1739-0.56745.54290.017-0.09010.32150.46780.0594-0.5149-0.34140.03-0.07080.377-0.03210.02510.4020.00520.336335.3893-2.4134-3.7044
51.933-1.51410.66636.73541.5351.41480.12110.3875-0.0291-0.7278-0.49-0.6477-0.11680.60260.350.6539-0.01570.19830.73020.02940.427519.4242-50.7714-35.3879
62.85952.3825-0.33367.1944-1.75733.15760.16280.6706-0.1782-1.056-0.4878-0.6813-0.28830.18610.3410.70880.0490.16380.70720.06960.402641.1727-6.8569-25.7472
72.4904-0.4584-0.62588.21171.91722.1964-0.06650.00240.1351-0.7894-0.22790.1443-0.0847-0.16490.25360.4753-0.0130.00810.60970.16110.458713.0032-4.8983-30.2641
82.5457-1.57120.24.8212-3.4495.48860.09940.1247-0.1369-0.993-0.0572-0.28780.5862-0.0968-0.07080.5985-0.02570.09180.5237-0.14070.324542.3759-52.883-19.0152
91.67090.2728-0.33462.32081.08331.62170.56940.4557-0.0239-0.1370.02771.31710.0603-0.0118-0.23730.51310.190.22010.84290.13980.845813.51635.2843-43.9045
104.7839-1.1505-1.40758.43376.01957.59440.13280.2086-0.36280.94730.092-0.60540.4355-0.0381-0.29190.64020.15070.04790.53340.06420.603154.7996-92.6604-27.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:90))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:90))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 91:186))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 91:186))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 192:285))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 192:285))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 286:379))
8X-RAY DIFFRACTION8chain 'B' and ((resseq 286:379))
9X-RAY DIFFRACTION9chain 'A' and ((resseq 380:475))
10X-RAY DIFFRACTION10chain 'B' and ((resseq 380:475))

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