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- PDB-4of0: Crystal Structure of SYG-1 D1-D2, refolded -

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Basic information

Entry
Database: PDB / ID: 4of0
TitleCrystal Structure of SYG-1 D1-D2, refolded
ComponentsProtein SYG-1, isoform b
KeywordsCELL ADHESION / Immunoglobulin superfamily / Synaptogenesis / Protein Binding / 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 / MAD / Resolution: 2.3 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

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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


Theoretical massNumber of molelcules
Total (without water)28,5821
Polymers28,5821
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.545, 32.065, 102.235
Angle α, β, γ (deg.)90.00, 113.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein SYG-1, isoform b


Mass: 28582.453 Da / Num. of mol.: 1 / Fragment: D1-D2, UNP residues 19-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: syg-1, CELE_K02E10.8, K02E10.8 / Plasmid: pHis-parallel1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B1Q236
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3,350, 0.2 M Ammonium acetate, 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: 8.2.1 / Wavelength: 0.9796,0.9797,0.9719
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97971
30.97191
ReflectionResolution: 2.3→50 Å / Num. obs: 11098 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 42.3 Å2 / Rsym value: 0.053 / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
BOSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1160)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→46.756 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 24.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 1143 10.3 %RANDOM
Rwork0.2008 ---
obs0.2053 11098 94.43 %-
all-11753 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 34 1827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051841
X-RAY DIFFRACTIONf_angle_d0.8082492
X-RAY DIFFRACTIONf_dihedral_angle_d11.209690
X-RAY DIFFRACTIONf_chiral_restr0.053282
X-RAY DIFFRACTIONf_plane_restr0.003321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40480.24541020.2166818X-RAY DIFFRACTION64
2.4048-2.53150.2861390.22491153X-RAY DIFFRACTION91
2.5315-2.69010.28891500.22141337X-RAY DIFFRACTION100
2.6901-2.89780.26511340.23581319X-RAY DIFFRACTION100
2.8978-3.18940.25781750.22541277X-RAY DIFFRACTION100
3.1894-3.65070.25091250.19811340X-RAY DIFFRACTION100
3.6507-4.59890.22111710.17531326X-RAY DIFFRACTION100
4.5989-46.76570.23841470.19511385X-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)
13.1639-0.3631.21481.4713-0.30046.7708-0.1704-1.2828-0.27791.09750.56240.78510.4948-1.5689-0.14011.380.1112-0.06711.2281-0.1790.435730.2793.343548.9162
22.69051.67131.66454.5342-2.66714.2544-1.303-2.09160.88971.62721.2436-0.5923-1.82611.42040.13731.37410.2659-0.36181.3888-0.32020.816235.878213.591648.4088
32.4446-0.56731.77860.8978-0.04399.2824-0.6624-1.18240.25750.86730.2554-0.2112-0.61360.30050.33360.74690.0509-0.06170.8775-0.05450.409331.04378.921838.2655
44.72440.20710.72164.21070.42526.5569-0.0066-0.4087-0.29850.54990.04730.31060.1966-0.1863-0.06310.23350.01620.08160.12810.00680.293815.67046.14368.7044
52.2542-1.585-2.29283.36321.0356.5635-0.006-0.683-0.34550.5777-0.19840.13940.7046-0.21780.12730.36730.01370.11520.23340.07550.421920.88311.5548.955
66.9114-0.80751.21984.36791.01675.4716-0.31360.26440.36640.0085-0.07870.4212-0.05370.16260.29260.25810.01860.07520.11160.00880.33515.64175.8373.0243
77.37070.15531.75945.97210.46532.33110.1155-0.77840.03450.6688-0.02280.2547-0.0343-0.3093-0.21750.21540.03640.12060.2674-0.04640.327513.51559.233811.9181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 268 )

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