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- PDB-5k6v: Sidekick-1 immunoglobulin domains 1-4, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 5k6v
TitleSidekick-1 immunoglobulin domains 1-4, crystal form 2
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 / MOLECULAR REPLACEMENT / Resolution: 3.208 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 / 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_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,10710
Polymers42,4821
Non-polymers1,6259
Water1086
1
A: Protein sidekick-1
hetero molecules

A: Protein sidekick-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,21420
Polymers84,9642
Non-polymers3,24918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area7880 Å2
ΔGint-342 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.189, 158.189, 53.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein sidekick-1


Mass: 42482.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unobserved N-terminal residues GPALA are from the expression vector and would be cleaved off in the native protein.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q3UH53

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Sugars , 3 types, 3 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 1
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 / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 2 types, 12 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#6: 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: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 7.5
Details: 10% PEG8000, 0.01M zinc chloride, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1.0052 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11639 / % possible obs: 90.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 70.26 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.2
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / % possible all: 72.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sdk1

Resolution: 3.208→34.74 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.1
RfactorNum. reflection% reflection
Rfree0.2441 568 4.88 %
Rwork0.2069 --
obs0.2088 11639 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.208→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 87 6 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023100
X-RAY DIFFRACTIONf_angle_d0.4894241
X-RAY DIFFRACTIONf_dihedral_angle_d13.861864
X-RAY DIFFRACTIONf_chiral_restr0.041496
X-RAY DIFFRACTIONf_plane_restr0.004544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2077-3.53020.34721160.28412294X-RAY DIFFRACTION76
3.5302-4.04040.29071590.22492647X-RAY DIFFRACTION88
4.0404-5.08790.19891440.17993003X-RAY DIFFRACTION99
5.0879-34.7420.22261490.19723127X-RAY DIFFRACTION100
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)
16.90994.94523.22323.75552.46831.74430.3775-0.8992-0.420.3325-0.4988-0.368-0.06510.28840.1140.5518-0.16330.09260.7360.06810.413454.4362-65.2431-1.4424
25.8619-0.9977-2.25014.3549-1.54826.4935-0.3057-0.4485-0.07870.32190.28190.1289-0.1008-0.14640.06240.4986-0.0941-0.01940.5068-0.02420.208317.3223-83.84116.0925
33.90743.32751.23877.28750.79114.5583-0.2278-0.10721.2011-0.2234-0.12510.2715-0.3046-0.00940.37520.55430.008-0.13720.6386-0.01440.49310.0785-62.70581.0727
41.47791.8276-0.23835.7554-1.15476.19980.5215-1.51521.42440.3564-0.5271.1491-0.2537-0.094-0.04710.6596-0.3370.2220.9324-0.33460.800552.4622-44.72416.8945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:90))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 91:189))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 190:285))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 286:379))

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