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- PDB-4of7: Crystal Structure of SYG-1 D1, Crystal Form 2 -

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Basic information

Entry
Database: PDB / ID: 4of7
TitleCrystal Structure of SYG-1 D1, Crystal Form 2
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: 2.1 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 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
C: Protein SYG-1, isoform b
D: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,53611
Polymers53,4884
Non-polymers1,0487
Water6,251347
1
A: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4682
Polymers13,3721
Non-polymers961
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)13,7854
Polymers13,3721
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5932
Polymers13,3721
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6893
Polymers13,3721
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.179, 129.179, 141.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-374-

HOH

21C-1012-

HOH

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Components

#1: Protein
Protein SYG-1, isoform b


Mass: 13371.917 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32.5% PEG 3,350, 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / 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: 2.1→50 Å / Num. all: 34516 / Num. obs: 34491 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 34.33 Å2 / Rsym value: 0.071 / Net I/σ(I): 25.6

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1265)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4OF0

4of0


Resolution: 2.1→44.302 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1721 4.99 %RANDOM
Rwork0.2017 ---
all0.203 35213 --
obs0.203 34491 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 62 347 3803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053513
X-RAY DIFFRACTIONf_angle_d0.9424758
X-RAY DIFFRACTIONf_dihedral_angle_d12.511315
X-RAY DIFFRACTIONf_chiral_restr0.066543
X-RAY DIFFRACTIONf_plane_restr0.004625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16010.27341190.25412288X-RAY DIFFRACTION84
2.1601-2.22980.29791140.24952600X-RAY DIFFRACTION93
2.2298-2.30950.31851340.25422715X-RAY DIFFRACTION99
2.3095-2.4020.28181500.25262758X-RAY DIFFRACTION100
2.402-2.51130.3271440.25862749X-RAY DIFFRACTION100
2.5113-2.64370.26181590.23872724X-RAY DIFFRACTION100
2.6437-2.80930.28131600.23442765X-RAY DIFFRACTION100
2.8093-3.02620.25421430.21732763X-RAY DIFFRACTION100
3.0262-3.33060.22421440.20232797X-RAY DIFFRACTION100
3.3306-3.81230.19651680.18642795X-RAY DIFFRACTION100
3.8123-4.80220.1851420.15182855X-RAY DIFFRACTION100
4.8022-44.31190.19271440.18792961X-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)
12.07925.39863.21635.3554-2.66392.4131-0.6888-0.32640.6393-0.18110.3060.4223-0.1928-1.05130.40680.3180.01550.02670.5139-0.04410.3887-44.2715.53279.7421
28.2719-1.00332.19483.5833-1.06826.28130.0075-0.2305-0.53580.2555-0.12530.04240.410.66120.16240.24380.00220.03950.25530.07430.1765-23.72226.24379.6694
35.8387-0.8061-0.49714.3959-1.81789.8359-0.2034-0.1047-0.24380.07960.00560.96390.4925-0.99680.10870.2556-0.08030.03090.3118-0.05440.3927-42.170214.1675.0298
42.20282.10986.19042.46152.82949.3783-0.15370.21171.3311-0.1811-0.26290.1419-1.09350.7110.45420.3372-0.06720.02120.29520.08950.3907-27.805720.17194.6854
57.0791-4.63930.56622.02392.04392.0271-0.0580.6425-0.0106-0.2317-0.49410.04320.832-0.52930.58360.4747-0.0426-0.02010.41790.11190.3522-33.054413.5669-4.9954
68.76131.2942-3.662.0251-1.7139.2219-0.5360.02750.3776-0.6537-0.5905-0.2034-0.8749-0.33220.80410.3258-0.0068-0.06640.29880.02690.4158-26.35114.9918-6.1609
79.68981.0893-7.71066.6175-3.6792.2457-0.27070.0226-0.0137-0.714-0.5715-0.09010.28540.06970.83950.27020.03570.00310.33630.01180.2439-24.850811.6244-1.9776
89.09825.98850.90878.37715.56375.7931-0.45030.6834-1.785-0.169-0.0490.68950.6876-0.99090.21460.3442-0.11080.05980.3712-0.08050.5039-39.85727.56190.9673
95.4555-0.70620.92274.1770.55712.95270.09731.0427-0.7994-0.7871-0.8540.25980.48841.06030.60480.27030.09840.19080.64420.22140.2074-22.70177.88682.2232
108.7926-1.2233-0.16692.6840.01513.45310.04680.31470.268-0.033-0.3687-0.1012-0.26820.63880.35610.2804-0.06070.02540.2650.0710.2559-23.838516.10718.2152
118.2979-4.0018.25877.8297-4.6352.7869-0.9516-1.33280.56680.53190.88970.2391-0.8551-1.35590.13910.36930.15830.03350.5142-0.00140.2803-40.741523.9947.5042
122.4821-7.2307-1.38327.09540.74552.5773-0.574-0.3089-0.47840.62980.0532-0.38080.17690.93950.66960.2855-0.00140.05790.53930.0840.4585-15.41815.643612.8145
135.9017-1.4278-3.21412.1072-2.08036.4352-1.24170.2628-0.5196-0.74550.8607-0.00320.4846-0.94210.27260.4483-0.1508-0.00010.50550.01610.649-40.3631-16.21221.5204
145.01782.9281-1.68437.2571-0.15724.26580.06830.43610.6438-0.2907-0.14370.1259-0.28270.10890.07390.22310.0328-0.04410.29330.1130.2803-22.6872-2.231219.5397
157.21374.8525-0.88669.655-0.74592.2160.4601-0.76140.12640.86610.01892.62470.2174-1.1638-0.26230.4207-0.0420.13170.62720.02330.7768-38.0722-14.182726.2069
162.09870.2736-3.52854.0417-1.32076.3691-0.0169-0.471-1.58450.3337-0.4553-0.22530.57580.60310.37570.39990.0053-0.06440.3260.0960.36-22.8041-16.226425.5867
177.5171.7225-2.70832.11185.8647.05950.0147-0.8837-0.66121.5136-0.50310.58320.6265-0.05620.40320.6987-0.1009-0.0740.50910.12280.5404-25.5819-10.467735.5077
182.0341-0.6166-0.62065.4758-1.83442.1169-0.4601-0.84780.17341.0498-0.1358-0.16920.12970.22770.66730.5201-0.00590.00570.45480.08390.2882-21.482-6.513531.4327
198.28832.913-0.31128.53120.95056.85910.0066-0.5615-0.60180.6545-0.37280.44950.5058-0.2370.31210.314-0.0052-0.02020.26730.09620.2787-27.5594-12.532124.9232
206.88585.7724-2.83657.9568-4.61779.14520.0073-0.12850.2539-0.535-0.8079-0.449-0.67050.36310.66220.33460.0277-0.06390.43750.11570.2951-15.5579-1.022115.8543
212.00218.4539.97782.00677.54749.0548-0.75341.4-0.1462-1.25830.8047-0.378-0.45211.22210.10780.5871-0.14330.13710.4276-0.07650.5371-18.910121.456628.478
226.09841.83361.50283.01851.9451.6165-0.09220.1731-0.74410.251-0.08540.16330.2506-0.07510.17880.2962-0.04290.13520.2673-0.09060.3598-36.59468.330623.6259
234.91842.34630.13894.71530.363.7768-0.4066-0.3153-0.56060.763-0.120.39510.1614-0.14090.4060.3754-0.00750.27660.315-0.12420.5153-42.63168.973630.2951
248.8014.50354.15756.05463.15293.0382-0.3691-0.1505-0.1708-0.14950.00820.6069-0.3293-0.31030.28630.2292-0.05960.18370.3087-0.12470.4842-42.425113.365623.3461
253.06964.0515-0.45439.5692-1.39029.1405-0.97010.9264-0.76130.1080.6289-0.99730.13171.2240.08110.3843-0.11230.03550.7792-0.31970.5333-25.2933-12.35416.5213
268.2771-6.5179-3.93576.33571.94046.610.34-0.41750.5327-0.408-0.38350.8381-0.73890.19670.07040.2901-0.015-0.07250.2786-0.12910.4282-42.9313-6.142213.2507
274.81410.99131.66096.46072.25366.3329-0.25940.4228-0.0632-1.25910.25540.2797-0.78830.6885-0.03610.6329-0.0988-0.13590.4221-0.15350.362-38.1892-10.61422.9699
286.369-2.10065.6337.5889-0.76636.39990.13140.82831.3283-3.1812-0.73070.4751-0.65640.57990.66021.36290.0479-0.44590.6146-0.09530.5149-43.8139-7.6039-4.6843
297.81033.5522-1.45265.58031.90177.0284-0.33521.27531.1245-2.33150.5381-0.0199-2.2181.323-0.09951.352-0.3979-0.00930.591-0.10040.3559-35.4322-3.28060.6753
308.66570.26050.43074.54180.28056.7284-0.53360.6891-1.4285-1.2554-0.11720.89310.11030.25040.47350.4976-0.039-0.12310.3351-0.25220.5067-39.9351-15.06693.9339
317.4763-5.475-3.83534.47772.36253.60060.20340.2990.4004-0.1304-0.57592.71450.9251-1.05760.2991-0.0885-0.106-0.05160.5486-0.321.6785-54.7135-3.32214.6955
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 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 72 )
7X-RAY DIFFRACTION7chain 'A' and (resid 73 through 79 )
8X-RAY DIFFRACTION8chain 'A' and (resid 80 through 87 )
9X-RAY DIFFRACTION9chain 'A' and (resid 88 through 95 )
10X-RAY DIFFRACTION10chain 'A' and (resid 96 through 106 )
11X-RAY DIFFRACTION11chain 'A' and (resid 107 through 119 )
12X-RAY DIFFRACTION12chain 'A' and (resid 120 through 129 )
13X-RAY DIFFRACTION13chain 'B' and (resid 21 through 27 )
14X-RAY DIFFRACTION14chain 'B' and (resid 28 through 42 )
15X-RAY DIFFRACTION15chain 'B' and (resid 43 through 52 )
16X-RAY DIFFRACTION16chain 'B' and (resid 53 through 62 )
17X-RAY DIFFRACTION17chain 'B' and (resid 63 through 72 )
18X-RAY DIFFRACTION18chain 'B' and (resid 73 through 79 )
19X-RAY DIFFRACTION19chain 'B' and (resid 80 through 119 )
20X-RAY DIFFRACTION20chain 'B' and (resid 120 through 128 )
21X-RAY DIFFRACTION21chain 'C' and (resid 16 through 23 )
22X-RAY DIFFRACTION22chain 'C' and (resid 24 through 52 )
23X-RAY DIFFRACTION23chain 'C' and (resid 53 through 106 )
24X-RAY DIFFRACTION24chain 'C' and (resid 107 through 129 )
25X-RAY DIFFRACTION25chain 'D' and (resid 21 through 27 )
26X-RAY DIFFRACTION26chain 'D' and (resid 28 through 35 )
27X-RAY DIFFRACTION27chain 'D' and (resid 36 through 62 )
28X-RAY DIFFRACTION28chain 'D' and (resid 63 through 79 )
29X-RAY DIFFRACTION29chain 'D' and (resid 80 through 91 )
30X-RAY DIFFRACTION30chain 'D' and (resid 92 through 119 )
31X-RAY DIFFRACTION31chain 'D' and (resid 120 through 130 )

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