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- PDB-4ofk: Crystal Structure of SYG-2 D4 -

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Basic information

Entry
Database: PDB / ID: 4ofk
TitleCrystal Structure of SYG-2 D4
ComponentsProtein SYG-2
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 / collateral sprouting / protein localization to synapse / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization / cell-cell adhesion ...Nephrin family interactions / synaptic target recognition / protein complex involved in cell adhesion / collateral sprouting / protein localization to synapse / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization / cell-cell adhesion / cell-cell junction / cell-cell signaling / protein homodimerization activity / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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 V-set domain / Immunoglobulin V-set domain / 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-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.802 Å
AuthorsOzkan, E. / Borek, D. / Otwinowski, Z. / 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 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SYG-2
B: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6338
Polymers22,9352
Non-polymers6986
Water2,576143
1
A: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7864
Polymers11,4681
Non-polymers3193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8474
Polymers11,4681
Non-polymers3793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.812, 54.131, 63.623
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1032-

HOH

21A-1052-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Protein SYG-2


Mass: 11467.713 Da / Num. of mol.: 2 / Fragment: D4, UNP residues 327-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26G2.1, CELE_C26G2.1, syg-2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9U3P2
#2: 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 , 4 types, 147 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 1.3 M Ammonium sulfate, 0.1 M Tris pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.16962 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.16962 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 18857 / Num. obs: 18855 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 23.11 Å2 / Rsym value: 0.051 / Net I/σ(I): 24.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.802→40.135 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 930 4.93 %Random
Rwork0.1913 ---
all0.1923 18854 --
obs0.1923 18854 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→40.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 42 143 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051666
X-RAY DIFFRACTIONf_angle_d1.0442277
X-RAY DIFFRACTIONf_dihedral_angle_d14.011615
X-RAY DIFFRACTIONf_chiral_restr0.043268
X-RAY DIFFRACTIONf_plane_restr0.006301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.802-1.89750.2381360.23822492X-RAY DIFFRACTION99
1.8975-2.01630.23471370.20932554X-RAY DIFFRACTION100
2.0163-2.1720.22241390.19932559X-RAY DIFFRACTION100
2.172-2.39060.21441470.19342532X-RAY DIFFRACTION100
2.3906-2.73640.21611150.19322585X-RAY DIFFRACTION100
2.7364-3.44730.24761260.19522581X-RAY DIFFRACTION100
3.4473-40.14530.17811300.17712621X-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)
11.62070.9833-0.47124.3248-2.847.0266-0.0510.1138-0.1966-0.19410.107-0.04730.8872-0.8092-0.02020.24320.0367-0.0140.2166-0.03780.2204-6.3084-12.4192-15.6384
21.94252.0105-2.19132.5778-1.79976.8835-0.21030.0892-0.3389-0.02380.0311-0.43490.5197-0.15430.11690.21090.1187-0.00160.1952-0.02880.1905-0.7277-10.2202-20.4762
33.37532.7225-5.78532.8874-4.09092.03240.0538-0.40140.06970.0314-0.2013-0.0449-0.33120.13360.10830.1950.068-0.01070.19850.01930.15841.3822-7.1616-12.1891
46.0885-0.0465-1.44790.77630.25290.4058-0.2001-1.1884-0.00480.15350.1589-0.17560.48250.7585-0.06260.25950.10040.00850.29590.01530.17712.2479-8.9337-7.5575
55.9273-0.16151.60226.5917-2.28089.6514-0.36950.59480.0164-0.7325-0.4846-0.0295-0.3876-0.87840.48420.2720.10970.02020.2826-0.06690.20733.8504-10.2951-29.5249
61.84232.5583-4.55683.7623-5.53032.0750.1001-0.2215-0.17460.1086-0.2252-0.22150.59170.26430.21480.26970.09950.00070.2329-0.00630.16420.8058-14.5-15.3724
79.3275-0.89580.87445.6121.73992.76750.2015-0.59780.08330.42020.13920.01420.2115-0.5198-0.24160.3232-0.06150.02280.26130.04420.1622-8.4578-14.80822.2754
82.0032.0021.97822.01821.99951.99630.55410.31210.5470.24060.20950.592-0.9896-0.792-0.71330.23610.10610.0720.17940.06290.2106-6.7368-8.4878-8.9016
98.38612.2067-2.34885.0734-0.43853.2120.13820.08120.39560.04310.02190.1735-0.4179-0.0418-0.22210.1890.0818-0.00130.1478-0.02050.15340.53260.8332-19.3807
109.13444.6859-3.14169.4859-8.17457.19910.5862-0.4592-0.16460.87280.08960.93240.207-0.8299-0.43120.4133-0.0280.04180.31530.0340.2488-12.6386-14.67-7.6161
112.65373.45720.51287.82172.38152.1173-0.13230.09840.3016-0.24920.22130.2039-0.34140.17550.03760.24820.1199-0.02930.2521-0.02490.246-5.164515.8902-18.696
124.38850.6231-1.10624.4236-0.43270.76170.1242-0.43790.34890.62340.058-0.2796-0.13430.1663-0.14860.30160.1322-0.02920.2943-0.05410.2167-6.880712.8937-14.5401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 327:346)
2X-RAY DIFFRACTION2chain 'A' and (resseq 347:361)
3X-RAY DIFFRACTION3chain 'A' and (resseq 362:367)
4X-RAY DIFFRACTION4chain 'A' and (resseq 368:377)
5X-RAY DIFFRACTION5chain 'A' and (resseq 378:385)
6X-RAY DIFFRACTION6chain 'A' and (resseq 386:395)
7X-RAY DIFFRACTION7chain 'A' and (resseq 396:405)
8X-RAY DIFFRACTION8chain 'A' and (resseq 406:410)
9X-RAY DIFFRACTION9chain 'A' and (resseq 411:420)
10X-RAY DIFFRACTION10chain 'A' and (resseq 421:429)
11X-RAY DIFFRACTION11chain 'B' and (resseq 327:354)
12X-RAY DIFFRACTION12chain 'B' and (resseq 355:430)

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