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- PDB-4of6: Crystal Structure of SYG-1 D1, Crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4of6
TitleCrystal Structure of SYG-1 D1, Crystal form 1
ComponentsProtein SYG-1, isoform b
KeywordsCELL ADHESION / Immunoglobulin superfamily / Synaptogenesis / Protein Binding / N-linked Glycosylation / Membrane / Extracellular / SIGNALING PROTEIN
Function / homology
Function and homology information


Nephrin family interactions / synaptic target recognition / protein complex involved in cell adhesion / branching morphogenesis of a nerve / collateral sprouting / actin filament bundle assembly / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization ...Nephrin family interactions / synaptic target recognition / protein complex involved in cell adhesion / branching morphogenesis of a nerve / collateral sprouting / actin filament bundle assembly / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization / cell-cell adhesion / cell-cell junction / cell-cell signaling / axon / synapse / protein-containing complex binding / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Synaptogenesis protein syg-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsOzkan, E. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis.
Authors: Ozkan, E. / Chia, P.H. / Wang, R.R. / Goriatcheva, N. / Borek, D. / Otwinowski, Z. / Walz, T. / Shen, K. / Garcia, K.C.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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 SYG-1, isoform b
B: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8687
Polymers26,7442
Non-polymers1,1245
Water4,918273
1
A: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0053
Polymers13,3721
Non-polymers6332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8634
Polymers13,3721
Non-polymers4913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.809, 84.809, 74.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1074-

HOH

21A-1075-

HOH

31B-1079-

HOH

41B-1122-

HOH

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Components

#1: Protein Protein SYG-1, isoform b


Mass: 13371.917 Da / Num. of mol.: 2 / Fragment: D1, UNP residues 19-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_K02E10.8, K02E10.8, syg-1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: B1Q236
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}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.: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 M Trisodium citrate, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2007
RadiationMonochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.696→50 Å / Num. all: 30393 / Num. obs: 30345 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 20.96 Å2 / Rsym value: 0.064 / Net I/σ(I): 32.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1160)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OF0

4of0


Resolution: 1.696→46.623 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1534 5.06 %RANDOM
Rwork0.1748 ---
obs0.1763 30345 99.39 %-
all-30345 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→46.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 74 273 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111842
X-RAY DIFFRACTIONf_angle_d1.3272494
X-RAY DIFFRACTIONf_dihedral_angle_d20.577720
X-RAY DIFFRACTIONf_chiral_restr0.1292
X-RAY DIFFRACTIONf_plane_restr0.006322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.696-1.75120.28651230.2442399X-RAY DIFFRACTION93
1.7512-1.81380.29721410.22222596X-RAY DIFFRACTION100
1.8138-1.88650.19781530.19142574X-RAY DIFFRACTION100
1.8865-1.97230.23651350.182603X-RAY DIFFRACTION100
1.9723-2.07630.19681400.16862598X-RAY DIFFRACTION100
2.0763-2.20640.19871430.16822599X-RAY DIFFRACTION100
2.2064-2.37670.20121260.18512632X-RAY DIFFRACTION100
2.3767-2.61590.24771280.19232650X-RAY DIFFRACTION100
2.6159-2.99440.23341530.17782637X-RAY DIFFRACTION100
2.9944-3.77230.17331320.16022694X-RAY DIFFRACTION100
3.7723-46.64060.18271600.16272829X-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)
13.8730.4834-0.66552.0051-1.11362.82070.0480.09550.3415-0.1035-0.1560.2815-0.3201-0.1664-0.01820.32970.05960.00490.1141-0.01080.181123.957736.689330.744
21.6947-0.0123-0.01481.46640.28531.6667-0.10830.0076-0.0671-0.29810.0229-0.0698-0.12120.08050.04960.21210.02570.05450.09390.01420.110429.504224.295827.2553
35.7295-0.2793-1.41944.41890.86115.1568-0.34830.5167-0.3156-0.62730.13870.1572-0.3074-0.64090.08950.5024-0.05850.06570.2249-0.02860.158728.750223.914815.0812
49.0184-3.8509-2.56135.1023.07231.8585-0.4330.4294-0.6172-0.22950.2212-0.106-0.392-0.14240.19130.3455-0.00110.10940.1637-0.02410.173730.486318.169518.4188
51.6120.2331-0.05472.43310.31821.9139-0.15890.0023-0.1545-0.4172-0.011-0.0376-0.001-0.00010.11770.24690.02020.08960.13080.00860.162529.988220.992625.3473
61.5596-0.19220.20541.7421-2.35823.5209-0.29040.0880.380.00470.0521-0.4116-1.22820.24170.22190.563-0.03010.00240.13310.01990.182332.496138.864927.2648
71.0426-0.7702-0.57781.67480.17450.7079-0.3107-0.2223-0.79060.0507-0.0018-0.12170.54440.0834-0.15120.19280.21610.22250.04940.07650.410434.50179.341133.1352
81.7640.0692-0.05643.76493.17512.6919-0.0432-0.52530.27270.25350.01330.0512-0.55920.14250.13480.4569-0.0803-0.01760.1897-0.05640.17658.141943.160810.6793
91.60390.22920.12612.6266-0.2221.4538-0.0605-0.0433-0.06730.2897-0.0123-0.0043-0.06310.08810.06920.149-0.0420.0520.1139-0.01350.136853.439525.50777.6477
101.67610.5336-1.0161.5462-0.92911.1474-0.1659-0.33630.01930.514-0.03960.1352-0.3470.1179-0.00450.3139-0.01330.09480.15570.0020.164345.676526.10415.8565
114.69292.228-0.81125.2649-1.18192.41180.046-0.3157-0.35630.5275-0.3635-0.1642-0.10540.02930.27320.2678-0.02770.08720.15090.02640.196448.192318.556316.5238
121.50580.0348-0.01141.8702-0.54232.1048-0.2071-0.1372-0.26780.31190.01030.00460.0163-0.02130.08960.181-0.0290.07470.10650.0020.214349.635922.656610.0782
130.76171.49091.12525.33973.87462.8199-0.0817-0.23160.27790.34310.01080.2352-0.5128-0.0550.03640.4079-0.02120.03430.1566-0.06940.175147.250440.673610.5216
142.84431.6341-1.05455.25550.19512.6822-0.45760.145-1.2-0.1021-0.0218-0.31530.88360.0145-0.00620.2669-0.13460.22520.173-0.09670.538146.09349.20380.7614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 119 )
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 79 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 119 )
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 131 )

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