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- PDB-4of8: Crystal Structure of Rst D1-D2 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4of8
TitleCrystal Structure of Rst D1-D2
ComponentsIrregular chiasm C-roughest protein
KeywordsCELL ADHESION / Immunoglobulin superfamily / myoblast fusion / eye development / Protein Binding / Membrane / Extracellular / Signaling Protein
Function / homology
Function and homology information


compound eye retinal cell programmed cell death / compound eye morphogenesis / regulation of striated muscle tissue development / compound eye development / retinal cell programmed cell death / myoblast fusion / homophilic cell adhesion via plasma membrane adhesion molecules / PDZ domain binding / adherens junction / apical part of cell ...compound eye retinal cell programmed cell death / compound eye morphogenesis / regulation of striated muscle tissue development / compound eye development / retinal cell programmed cell death / myoblast fusion / homophilic cell adhesion via plasma membrane adhesion molecules / PDZ domain binding / adherens junction / apical part of cell / membrane => GO:0016020 / apical plasma membrane / identical protein 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
Irregular chiasm C-roughest protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Irregular chiasm C-roughest protein
B: Irregular chiasm C-roughest protein
C: Irregular chiasm C-roughest protein
D: Irregular chiasm C-roughest protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,76214
Polymers102,1184
Non-polymers64510
Water15,187843
1
A: Irregular chiasm C-roughest protein
D: Irregular chiasm C-roughest protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4738
Polymers51,0592
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Irregular chiasm C-roughest protein
C: Irregular chiasm C-roughest protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2896
Polymers51,0592
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.941, 77.935, 121.097
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Irregular chiasm C-roughest protein / Protein IRREC


Mass: 25529.479 Da / Num. of mol.: 4 / Fragment: D1-D2, UNP residues 20-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG4125, rst / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q08180
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 55.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG 3,350, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 77258 / Num. obs: 77176 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 21.27 Å2 / Rsym value: 0.066 / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4OF0
Resolution: 1.902→44.57 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 3893 5.04 %
Rwork0.1727 --
obs0.1746 77175 88.48 %
all-87224 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.2696 Å2-0 Å22.3725 Å2
2---9.1406 Å20 Å2
3----12.129 Å2
Refinement stepCycle: LAST / Resolution: 1.902→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 40 843 7427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016755
X-RAY DIFFRACTIONf_angle_d0.9669126
X-RAY DIFFRACTIONf_dihedral_angle_d12.1552548
X-RAY DIFFRACTIONf_chiral_restr0.041016
X-RAY DIFFRACTIONf_plane_restr0.0051214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-1.92570.3108670.23611405X-RAY DIFFRACTION47
1.9257-1.95010.2651720.1961593X-RAY DIFFRACTION54
1.9501-1.97570.1861670.19821717X-RAY DIFFRACTION57
1.9757-2.00280.22231060.20081826X-RAY DIFFRACTION62
2.0028-2.03140.2261110.19762009X-RAY DIFFRACTION69
2.0314-2.06170.25081060.20162182X-RAY DIFFRACTION73
2.0617-2.09390.21671170.19452294X-RAY DIFFRACTION78
2.0939-2.12830.22651260.19042351X-RAY DIFFRACTION80
2.1283-2.1650.22261210.18212503X-RAY DIFFRACTION84
2.165-2.20430.27081630.1972545X-RAY DIFFRACTION88
2.2043-2.24670.23511450.19052695X-RAY DIFFRACTION92
2.2467-2.29260.21611420.19472865X-RAY DIFFRACTION96
2.2926-2.34240.24431590.19372857X-RAY DIFFRACTION98
2.3424-2.39690.22091580.19482924X-RAY DIFFRACTION99
2.3969-2.45690.20551320.18122963X-RAY DIFFRACTION100
2.4569-2.52330.23561620.18362953X-RAY DIFFRACTION100
2.5233-2.59750.25421680.17742962X-RAY DIFFRACTION100
2.5975-2.68140.19061650.18732895X-RAY DIFFRACTION100
2.6814-2.77720.21611480.17362957X-RAY DIFFRACTION100
2.7772-2.88840.2321590.17822975X-RAY DIFFRACTION100
2.8884-3.01980.22651810.18942920X-RAY DIFFRACTION100
3.0198-3.17890.20871590.17312971X-RAY DIFFRACTION100
3.1789-3.37810.22481800.16582936X-RAY DIFFRACTION100
3.3781-3.63880.1821480.1572965X-RAY DIFFRACTION100
3.6388-4.00470.18711570.16552985X-RAY DIFFRACTION100
4.0047-4.58370.16251520.13442994X-RAY DIFFRACTION100
4.5837-5.7730.17071540.14582993X-RAY DIFFRACTION100
5.773-44.5820.21461680.18483047X-RAY DIFFRACTION100
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)
11.1378-0.1409-0.2522.2929-0.05243.27150.02480.0091-0.06710.1372-0.07120.13590.2479-0.06670.05520.1013-0.01310.00030.0875-0.01720.144-6.7497-29.001256.5918
21.59511.2770.02213.5413-1.31462.4793-0.01430.13210.0865-0.1519-0.0824-0.4812-0.62730.67830.05010.2614-0.09390.02790.33830.01410.2916.3163-9.698230.2253
32.6951.4016-0.30774.6185-1.36144.5248-0.25350.37970.1445-0.90010.1001-0.6163-0.07941.14320.16780.3438-0.08770.08990.48020.03350.272719.1764-10.066621.9658
40.9070.28350.64533.08930.94611.5827-0.13170.0378-0.3705-0.00440.0578-0.16390.83530.10310.13130.35440.0252-0.03450.1112-0.00890.19682.7768-34.68259.8501
51.38380.3459-1.10991.04110.27334.13250.0064-0.1030.01480.05040.0059-0.12770.06560.207-0.00670.2114-0.0005-0.04060.12190.00290.16254.8942-24.573313.1658
63.34361.5465-1.32553.4648-1.03675.3016-0.31650.3868-0.302-0.30610.0599-0.30240.44150.11070.26990.24950.00520.0080.1409-0.00940.15966.0796-30.1928-1.59
71.9577-0.1969-1.04571.61630.96832.81490.0902-0.24960.4387-0.0665-0.1230.59290.0057-1.3881-0.01860.03320.0919-0.02310.9555-0.09650.4907-26.1518-19.011139.1728
83.3110.6868-2.02872.1063-0.88483.174-0.0559-0.3831-0.0944-0.0468-0.03550.79120.6261-0.7550.11980.2086-0.1052-0.02340.6881-0.03160.4503-25.5539-28.328238.8655
96.69594.0442-3.11916.8383-2.79235.21450.20720.79560.7885-0.84710.05780.915-0.2535-1.4272-0.23370.41970.1617-0.13950.7256-0.01130.4222-22.6677-19.349425.7607
103.13490.20981.47072.37711.77521.84350.6614-1.0142-0.04620.8277-0.34731.02410.5378-1.3056-0.25030.1057-0.0903-0.09791.26780.09090.6421-33.7244-22.862944.1569
114.39410.2628-1.88562.6594-0.15533.46190.1059-0.5650.00220.1111-0.0770.38130.5337-0.5667-0.01350.2578-0.0846-0.05470.4312-0.02140.2148-18.5196-27.090340.4242
128.07240.6989-3.3623.49690.01385.7645-0.0375-1.01870.7150.6351-0.26481.0739-0.2018-1.21760.2573-0.15840.0584-0.19891.125-0.27780.4711-28.1707-19.596549.8518
131.24-0.1895-0.11941.00880.12663.05590.0459-0.00270.09810.1153-0.0432-0.0559-0.17130.058-0.00630.2666-0.015-0.00250.07820.01480.14941.5804-11.2447-3.534
142.6471.0081.484.19823.9985.7489-0.07260.4496-0.3534-0.08890.1898-0.07810.29630.0652-0.15640.3163-0.05190.03650.1955-0.03090.2316-8.7066-26.889-29.3675
152.2448-0.13110.85093.81112.09765.1836-0.05831.3663-1.1734-0.54210.43080.39570.8958-1.2512-0.34680.6298-0.4626-0.03061.0488-0.24380.5889-21.481-37.3598-44.7192
167.5437-0.70016.41482.36980.4272.0284-0.18620.3422-0.0944-0.10230.22890.2681-0.3172-0.20840.05870.2762-0.08950.03560.30620.03460.1988-15.198-24.9385-30.999
176.0601-1.01432.17474.4844-2.16166.1058-0.230.5035-0.06420.28960.10940.5682-0.1094-0.34690.1740.3227-0.05010.07380.3173-0.01920.3534-18.9176-28.1219-30.9959
183.90280.11810.08953.45392.23293.3469-0.12431.4211-0.2052-0.83060.17160.71120.1581-1.0767-0.03490.6331-0.2867-0.0310.96850.00470.43-22.937-32.313-43.4237
195.34060.38211.36494.52870.87334.9561-0.29270.73090.0485-0.91730.5030.291-0.4132-0.4869-0.23080.4057-0.0821-0.00430.34590.05870.1941-12.833-21.4167-36.8023
206.19481.05613.10786.00891.66677.8709-0.19221.4507-1.14-0.92940.35570.29820.6958-0.7177-0.18330.5914-0.34160.08640.759-0.25860.4651-15.5155-31.6861-47.9927
211.04870.6432-0.76652.3979-0.68763.4250.00690.01360.33770.07930.05050.1465-0.895-0.08280.02350.19980.02090.04660.113-0.00660.2112-10.0394-5.409469.6688
221.30370.508-0.26851.4549-0.11873.32230.0131-0.0852-0.01570.1532-0.00410.25780.0947-0.2722-0.00810.1583-0.01610.02650.1227-0.01050.1882-13.9795-15.733572.8859
230.9170.4341-1.29123.5231-0.65584.0462-0.02070.25710.0854-0.0186-0.03480.2741-0.1126-0.24630.06870.0710.01160.00940.13790.00490.175-8.9535-11.485862.0126
242.9209-0.8481.55152.1895-1.56393.5410.0267-0.5963-0.1430.4931-0.2048-0.59250.10711.21190.05370.29530.023-0.14270.87670.10120.373912.7137-20.9882103.9957
252.13960.52742.27152.73781.91555.3222-0.0645-0.6810.30450.3176-0.1767-0.5604-0.63751.15140.15340.4168-0.2358-0.06760.8241-0.02610.330912.2503-11.6254103.1052
268.17193.29413.89458.47195.5369.05710.02250.5379-0.7399-0.5174-0.1002-0.5424-0.13381.62370.02330.52420.09840.07470.76240.06460.351711.8909-20.905389.9983
272.4606-0.13540.95511.0966-1.39642.12180.1486-0.87250.15850.8461-0.1456-0.529-0.58041.3650.0460.6808-0.1051-0.13651.48560.04080.526619.3329-16.9772110.0655
283.5454-0.55441.88683.2978-0.59314.5825-0.1991-0.8024-0.0520.56930.11-0.5289-0.88710.77190.08850.3649-0.0849-0.02850.66530.04570.24978.107-15.758108.0414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 235 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 40 )
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 123 )
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 157 )
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 179 )
9X-RAY DIFFRACTION9chain 'B' and (resid 180 through 192 )
10X-RAY DIFFRACTION10chain 'B' and (resid 193 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 224 )
12X-RAY DIFFRACTION12chain 'B' and (resid 225 through 234 )
13X-RAY DIFFRACTION13chain 'C' and (resid 25 through 123 )
14X-RAY DIFFRACTION14chain 'C' and (resid 124 through 141 )
15X-RAY DIFFRACTION15chain 'C' and (resid 142 through 157 )
16X-RAY DIFFRACTION16chain 'C' and (resid 158 through 169 )
17X-RAY DIFFRACTION17chain 'C' and (resid 170 through 192 )
18X-RAY DIFFRACTION18chain 'C' and (resid 193 through 209 )
19X-RAY DIFFRACTION19chain 'C' and (resid 210 through 224 )
20X-RAY DIFFRACTION20chain 'C' and (resid 225 through 234 )
21X-RAY DIFFRACTION21chain 'D' and (resid 26 through 40 )
22X-RAY DIFFRACTION22chain 'D' and (resid 41 through 102 )
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 123 )
24X-RAY DIFFRACTION24chain 'D' and (resid 124 through 157 )
25X-RAY DIFFRACTION25chain 'D' and (resid 158 through 179 )
26X-RAY DIFFRACTION26chain 'D' and (resid 180 through 192 )
27X-RAY DIFFRACTION27chain 'D' and (resid 193 through 209 )
28X-RAY DIFFRACTION28chain 'D' and (resid 210 through 234 )

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