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- PDB-5k6u: Sidekick-1 immunoglobulin domains 1-4, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5k6u
TitleSidekick-1 immunoglobulin domains 1-4, crystal form 1
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
: / IODIDE ION / Protein sidekick-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 Å
AuthorsJin, X. / Goodman, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,22510
Polymers42,4821
Non-polymers1,7439
Water2,666148
1
A: Protein sidekick-1
hetero molecules

A: Protein sidekick-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,45120
Polymers84,9642
Non-polymers3,48618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-23 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.072, 49.260, 60.728
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein sidekick-1


Mass: 42482.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GPALA are from the expression construct 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
#2: 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
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 295 K / Method: batch mode / Details: 12-16% (w/v) PEG4000, 0.2M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.7432 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7432 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22884 / % possible obs: 98.63 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.56 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.201→38.186 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2284 1175 5.13 %
Rwork0.1912 --
obs0.1931 22884 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→38.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 63 148 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073081
X-RAY DIFFRACTIONf_angle_d0.884226
X-RAY DIFFRACTIONf_dihedral_angle_d12.1851143
X-RAY DIFFRACTIONf_chiral_restr0.054496
X-RAY DIFFRACTIONf_plane_restr0.005542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2015-2.30170.33861340.28792693X-RAY DIFFRACTION97
2.3017-2.4230.32071570.2492704X-RAY DIFFRACTION100
2.423-2.57480.23691540.22132725X-RAY DIFFRACTION100
2.5748-2.77350.30571570.22082713X-RAY DIFFRACTION100
2.7735-3.05250.25131460.19592730X-RAY DIFFRACTION100
3.0525-3.49390.2081180.18592760X-RAY DIFFRACTION99
3.4939-4.4010.19411580.15952669X-RAY DIFFRACTION97
4.401-38.1920.19721510.17382715X-RAY DIFFRACTION96
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)
14.6042-3.33883.75592.1743-1.52512.36420.01090.34460.22440.0271-0.0483-0.29630.04130.09880.07150.2386-0.0020.00930.3280.010.2466-20.9723-22.039517.1615
28.78514.0756-0.84423.7383-0.54561.9347-0.08170.3918-0.3684-0.28930.1719-0.13640.0684-0.0175-0.0840.30650.03930.00680.15270.00930.17520.8689-21.792318.2751
34.26642.33260.83161.31780.27321.9915-0.1456-0.01291.3310.01460.06120.8694-0.1312-0.3330.06890.35150.02610.03410.22920.05660.651515.35920.667318.761
44.1061-0.58280.99433.2111-0.30063.89250.0480.09820.4422-0.1875-0.2343-0.4775-0.18280.18670.16670.3157-0.02760.0630.28270.03290.252-26.5371-3.07366.3166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 379 )

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