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- PDB-5k70: Sidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant -

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Basic information

Entry
Database: PDB / ID: 5k70
TitleSidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant
ComponentsProtein sidekick-2
KeywordsCELL ADHESION / immunoglobulin
Function / homology
Function and homology information


SDK interactions / camera-type eye photoreceptor cell differentiation / retina layer formation / homophilic cell-cell adhesion / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein sidekick-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Protein sidekick-2
D: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,19125
Polymers169,5254
Non-polymers3,66621
Water1,11762
1
A: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7439
Polymers42,3811
Non-polymers1,3628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3507
Polymers42,3811
Non-polymers9686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1605
Polymers42,3811
Non-polymers7784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9384
Polymers42,3811
Non-polymers5573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.890, 113.430, 185.906
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein sidekick-2


Mass: 42381.191 Da / Num. of mol.: 4 / Mutation: H18R/N22S mutant
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GPAGA are expression construct-derived and would be cleaved in the native protein
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk2, Kiaa1514 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6V4S5

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Sugars , 3 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
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
#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.: 3
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, 76 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 13.5% PEG3350 (w/v), 0.1M ammonium sulfate, 0.2M sodium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→65 Å / Num. obs: 61442 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sdk1

Resolution: 2.7→39.516 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.2434 3112 5.06 %
Rwork0.206 --
obs0.2079 61442 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 222 62 11595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411806
X-RAY DIFFRACTIONf_angle_d1.06416146
X-RAY DIFFRACTIONf_dihedral_angle_d13.2554263
X-RAY DIFFRACTIONf_chiral_restr0.041886
X-RAY DIFFRACTIONf_plane_restr0.0042086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74220.37121440.31822615X-RAY DIFFRACTION100
2.7422-2.78710.37841500.30952622X-RAY DIFFRACTION100
2.7871-2.83520.3681540.29182649X-RAY DIFFRACTION100
2.8352-2.88670.32331430.28292616X-RAY DIFFRACTION100
2.8867-2.94220.31011190.28032675X-RAY DIFFRACTION100
2.9422-3.00230.311530.26462635X-RAY DIFFRACTION100
3.0023-3.06750.2861170.24782653X-RAY DIFFRACTION100
3.0675-3.13880.27751540.24612633X-RAY DIFFRACTION100
3.1388-3.21730.26221460.242625X-RAY DIFFRACTION100
3.2173-3.30420.28011430.23452655X-RAY DIFFRACTION100
3.3042-3.40140.2441250.23322638X-RAY DIFFRACTION100
3.4014-3.51110.3031500.22382657X-RAY DIFFRACTION100
3.5111-3.63660.25441270.21072641X-RAY DIFFRACTION100
3.6366-3.7820.25031450.20652674X-RAY DIFFRACTION100
3.782-3.9540.26831560.18892624X-RAY DIFFRACTION100
3.954-4.16230.20611520.17792639X-RAY DIFFRACTION100
4.1623-4.42270.17641420.16042648X-RAY DIFFRACTION100
4.4227-4.76370.16441230.14662680X-RAY DIFFRACTION100
4.7637-5.24210.1991520.15962654X-RAY DIFFRACTION100
5.2421-5.99840.2061510.172662X-RAY DIFFRACTION100
5.9984-7.54870.23811360.19822693X-RAY DIFFRACTION100
7.5487-39.520.19051300.18782742X-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)
16.45110.10461.07310.72540.24661.7960.0546-0.29230.01270.02690.01240.0268-0.0210.0169-0.04460.27220.03210.03840.32920.00360.2032-15.0158-37.4761-5.6012
24.6236-1.85631.9994.8155-1.0573.91390.24270.0089-0.7405-0.0443-0.0428-0.08380.64910.2464-0.15030.41330.0075-0.020.3028-0.02130.3063-32.3609-49.1508-35.4935
31.50680.1894-0.8771.3624-0.41983.6725-0.1997-0.46110.02590.15590.3340.2617-0.3066-1.2-0.12770.6572-0.0013-0.03850.9913-0.00750.3211-83.0119-48.9784-75.0881
42.4618-0.61691.29215.1516-0.77872.6439-0.18490.11760.28160.0191-0.0044-0.0134-0.3938-0.04640.26410.3722-0.0938-0.04910.3588-0.05120.2878-53.8861-37.6695-56.99
53.5675-0.73250.96521.2668-0.33443.1427-0.0503-0.2374-0.19670.010.08880.0864-0.095-0.1684-0.03750.27640.00970.01260.26620.00530.266-55.2639-27.3511-14.1339
64.9236-0.42491.49672.5791-0.6591.60380.23190.5125-0.99320.0610.0290.13280.49310.2405-0.17990.45630.1174-0.0190.4193-0.09160.45313.6701-66.5838-20.4198
74.3983-1.34190.56662.37940.65923.4379-0.0176-0.3966-0.40040.58810.07540.34230.0508-0.7809-0.0760.716-0.14950.08730.6155-0.02410.322-74.4566-61.178-35.1749
80.8010.05050.14880.1062-0.01980.3919-0.8323-0.17981.2018-1.2668-0.21250.3439-2.8476-0.13940.23842.6672-0.0115-0.49260.18620.38880.5382-68.3555-19.224-92.5044
94.9247-1.1117-0.88061.65720.57721.6819-0.0140.43130.2351-0.21170.0259-0.1177-0.3148-0.0014-0.01150.35670.0075-0.03390.22960.01760.214-45.3288-19.2046-33.0835
101.1514-1.21210.38192.4760.29691.78940.24010.75950.3608-0.2799-0.2826-0.5011-0.01130.28190.05030.3350.07540.07070.64090.01960.334210.9018-45.2973-23.5611
113.94590.6626-0.03514.0928-0.62313.4771-0.0029-0.2499-0.63620.26920.1382-0.35860.39640.1893-0.12060.5115-0.0808-0.05930.3196-0.00860.4146-55.2452-68.3578-45.6569
120.90060.521-0.73710.8647-0.92852.1035-0.34070.84140.0031-1.1772-0.0604-0.2955-0.5970.43240.45991.2447-0.18750.04190.80350.07280.4211-64.861-40.0236-100.0439
134.3152-0.53941.24772.8155-0.05281.2633-0.33530.66931.7442-0.0485-0.205-0.6733-0.49440.65160.40740.4394-0.0997-0.07470.44810.14140.7067-2.7844-22.9715-16.7537
143.8296-0.53791.74770.88250.07622.9387-0.19250.72760.4551-0.2163-0.0462-0.17070.12110.34410.22520.3399-0.09840.03640.58260.08950.2932-25.9936-30.8561-46.9276
151.15-0.32850.89150.7725-0.34032.51380.06810.3658-0.1596-1.30710.1752-0.15080.45760.2244-0.23241.0674-0.21650.01650.5081-0.04210.3895-70.9539-62.5048-88.1285
161.93670.10711.61571.7390.09213.46920.14360.7384-0.2845-0.39390.2143-0.48450.71891.1047-0.38340.5024-0.01690.04910.744-0.25440.4443-41.8966-54.8238-64.1727
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 'C' and ((resseq 1:90))
4X-RAY DIFFRACTION4chain 'D' and ((resseq 1:90))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 91:184))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 91:184))
7X-RAY DIFFRACTION7chain 'C' and ((resseq 91:184))
8X-RAY DIFFRACTION8chain 'D' and ((resseq 91:183))
9X-RAY DIFFRACTION9chain 'A' and ((resseq 192:285))
10X-RAY DIFFRACTION10chain 'B' and ((resseq 192:285))
11X-RAY DIFFRACTION11chain 'C' and ((resseq 192:285))
12X-RAY DIFFRACTION12chain 'D' and ((resseq 193:285))
13X-RAY DIFFRACTION13chain 'A' and ((resseq 286:379))
14X-RAY DIFFRACTION14chain 'B' and ((resseq 286:379))
15X-RAY DIFFRACTION15chain 'C' and ((resseq 286:379))
16X-RAY DIFFRACTION16chain 'D' and ((resseq 286:378))

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