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- PDB-5k6x: Sidekick-2 immunoglobulin domains 1-4, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5k6x
TitleSidekick-2 immunoglobulin domains 1-4, crystal form 1
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 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
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 / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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-2
B: Protein sidekick-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40319
Polymers84,7782
Non-polymers2,62517
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-129 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.110, 130.010, 78.390
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein sidekick-2


Mass: 42389.168 Da / Num. of mol.: 2
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 / Production host: Homo sapiens (human) / References: UniProt: Q6V4S5

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
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)-[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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.26 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4 / Details: 1.5M ammonium sulfate, 0.1M sodium citrate pH4

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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: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 29407 / % possible obs: 98.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.8 / % possible all: 98.5

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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→39.002 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2299 1486 5.05 %
Rwork0.1926 --
obs0.1946 29407 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 156 38 5843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035947
X-RAY DIFFRACTIONf_angle_d0.7058130
X-RAY DIFFRACTIONf_dihedral_angle_d12.3722149
X-RAY DIFFRACTIONf_chiral_restr0.026947
X-RAY DIFFRACTIONf_plane_restr0.0031038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.78720.33321290.27562525X-RAY DIFFRACTION98
2.7872-2.88680.30551290.26062541X-RAY DIFFRACTION98
2.8868-3.00240.29591260.24082517X-RAY DIFFRACTION99
3.0024-3.1390.26151390.22282539X-RAY DIFFRACTION99
3.139-3.30440.29721410.20782496X-RAY DIFFRACTION99
3.3044-3.51130.23911290.19592552X-RAY DIFFRACTION99
3.5113-3.78220.21981280.18792540X-RAY DIFFRACTION99
3.7822-4.16240.21371610.16692539X-RAY DIFFRACTION99
4.1624-4.76380.18131190.15362559X-RAY DIFFRACTION99
4.7638-5.99840.18911450.17552551X-RAY DIFFRACTION99
5.9984-39.00640.22791400.20212562X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.06010.95412.81163.04320.88013.8631-0.0022-0.28130.36770.2371-0.1403-0.0258-0.42030.02310.17390.4506-0.0998-0.00440.34-0.03620.2904-7.913131.975213.8006
22.326-0.19271.96171.5996-1.30342.5051-0.09680.12150.0270.01380.12680.0676-0.7614-0.2741-0.01050.48680.0357-0.03730.588-0.05550.3898-23.25727.2672-25.2734
31.4277-0.2023-0.2681.79310.15231.6991-0.13060.19180.0470.06610.2455-0.248-0.14480.4456-0.10080.6542-0.1476-0.10720.4495-0.02650.48959.970442.942810.5828
41.58010.244-0.48332.93580.92376.6437-0.03280.2263-0.1131-0.02250.01790.05720.5996-0.13450.02670.3536-0.0698-0.03210.3386-0.05710.3778-16.79268.8644-8.7077
54.9945-0.36433.46181.71770.29074.09820.2537-0.4169-0.58110.2341-0.0059-0.00190.1392-0.2043-0.24230.4245-0.1026-0.0060.45040.08290.35975.606514.524626.5485
64.99070.0516-1.26423.05761.00756.5248-0.00490.0994-0.0108-0.1597-0.0481-0.1082-0.347-0.30510.04740.3459-0.02950.02810.3569-0.00840.386120.437419.246110.0466
71.58070.16330.54110.9473-0.42951.6535-0.17710.37590.017-0.50410.212-0.17410.04130.4675-0.12640.54620.0226-0.05070.6248-0.11710.4694-1.71362.9436-21.7488
83.89771.1193-0.123.22190.62161.073-0.13250.8913-0.1141-0.1080.1104-0.477-0.47080.7996-0.01130.7043-0.161-0.14171.0194-0.12480.557-0.962127.7808-28.3601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 379 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 90 )
5X-RAY DIFFRACTION5chain 'B' and (resid 91 through 185 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 285 )
7X-RAY DIFFRACTION7chain 'B' and (resid 286 through 378 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 285 )

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