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- PDB-5y3c: Crystal structure of zebrafish Ccd1 DIX domain -

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Basic information

Entry
Database: PDB / ID: 5y3c
TitleCrystal structure of zebrafish Ccd1 DIX domain
ComponentsDixin-A
KeywordsSIGNALING PROTEIN / Wnt signal
Function / homology
Function and homology information


camera-type eye development / canonical Wnt signaling pathway / forebrain development / focal adhesion / identical protein binding / cytosol
Similarity search - Function
Ribosomal Protein L25; Chain P - #130 / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Ribosomal Protein L25; Chain P / Ubiquitin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTerawaki, S. / Shibata, N. / Higuchi, Y.
Funding support Japan, 17items
OrganizationGrant numberCountry
MEXT22121519 Japan
MEXT23121527 Japan
MEXT25121705 Japan
MEXT23121526 Japan
MEXT25121731 Japan
JSPS22370061 Japan
JSPS22770112 Japan
JSPS25840017 Japan
Hyogo Science and Technology Association Japan
Sasakawa Scienti c Research Grant from the Japan Science Society Japan
Sumitomo Foundation
Leave a Nest Grants Caliper Life Science Award Japan
Uehara Memorial Foundation Japan
Takeda Medical Science Japan
Inamori Foundation Japan
JAXA Japan
Grant-in-Aid from the Global COE program Japan
Citation
Journal: Sci Rep / Year: 2017
Title: Structural basis for Ccd1 auto-inhibition in the Wnt pathway through homomerization of the DIX domain.
Authors: Terawaki, S.I. / Fujita, S. / Katsutani, T. / Shiomi, K. / Keino-Masu, K. / Masu, M. / Wakamatsu, K. / Shibata, N. / Higuchi, Y.
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2007
Title: The DIX domain of Dishevelled confers Wnt signaling by dynamic polymerization.
Authors: Schwarz-Romond, T. / Fiedler, M. / Shibata, N. / Butler, P.J. / Kikuchi, A. / Higuchi, Y. / Bienz, M.
History
DepositionJul 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dixin-A


Theoretical massNumber of molelcules
Total (without water)9,5991
Polymers9,5991
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5590 Å2
Unit cell
Length a, b, c (Å)46.724, 46.724, 79.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Dixin-A / Coiled-coil protein DIX1-A / Coiled-coil-DIX1-A / DIX domain-containing protein 1-A


Mass: 9598.747 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 356-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: dixdc1a, ccd1, dixdc1 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q804T6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14% poly(acrylic acid sodium salt) 5100, 100 mM HEPES-Na (pH 7.5), 20 mM MgCl2, 10 mM TCEP-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 7076 / % possible obs: 99.1 % / Redundancy: 9 % / Net I/σ(I): 35.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y3B

5y3b


Resolution: 1.96→23.362 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.06
RfactorNum. reflection% reflection
Rfree0.2158 722 10.23 %
Rwork0.1692 --
obs0.1739 7061 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→23.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 0 66 734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004687
X-RAY DIFFRACTIONf_angle_d0.757933
X-RAY DIFFRACTIONf_dihedral_angle_d8.947246
X-RAY DIFFRACTIONf_chiral_restr0.029101
X-RAY DIFFRACTIONf_plane_restr0.003119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.956-2.10690.23531400.18931226X-RAY DIFFRACTION97
2.1069-2.31880.24151430.18351274X-RAY DIFFRACTION99
2.3188-2.65390.26541410.18131264X-RAY DIFFRACTION99
2.6539-3.34210.23241540.18081284X-RAY DIFFRACTION100
3.3421-23.36370.18091440.15171291X-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)
12.33881.22411.61370.63310.84091.11170.04330.43911.8304-0.62260.211-0.4057-1.42250.95440.39290.9418-0.46590.25940.6899-0.18681.010525.559227.85865.9851
28.78195.51960.31648.42772.9192.6046-0.5541-0.0115-0.2915-0.52840.2579-0.0254-0.38820.0110.25080.1614-0.0304-0.01890.14370.01380.140312.946512.87575.2741
30.8373-2.523-1.82519.81478.79748.9951-0.6252-1.0435-2.70051.9085-0.23731.88741.6216-1.06610.28830.4707-0.010.11930.36490.17530.83494.30847.23928.1844
44.68534.2653-1.06425.86792.15847.974-0.0588-0.42970.6299-0.12820.3640.3183-0.68530.8637-0.16810.2571-0.0232-0.03790.1766-0.00170.230114.226316.81638.6993
52.0205-5.22780.85579.87436.63626.92180.30340.03690.7398-0.2339-0.3102-1.0545-1.32071.93060.43860.175-0.3622-0.09820.8220.10510.315726.979316.94954.4193
63.5095-4.8153-0.48957.38112.97926.7348-0.5499-0.00080.3710.28350.4348-0.3316-0.07510.48640.09750.1576-0.0615-0.04720.31680.01540.197422.087710.062711.368
75.9496-3.1928-3.28999.7255.80913.8467-1.3732-2.00240.29112.91930.83050.40492.3274-0.20280.11180.76890.2244-0.08730.70030.1170.580415.73854.283616.1091
82.90030.9746-1.30847.6167-2.18927.5866-0.4155-0.0865-0.5492-0.1556-0.1969-0.370.60920.58470.46080.19550.00460.05110.15320.02880.206418.77644.5421-0.5775
97.28390.0556-0.20726.63240.74132.3201-0.22010.1352-0.1318-0.54910.0413-0.48880.34220.66040.30930.29530.0640.08810.20230.02810.214619.89712.8784-7.8821
106.73022.1989-2.12273.2321.07966.34950.1129-0.0084-0.5457-0.55920.1055-0.23830.55451.0042-0.23020.21450.0205-0.00450.43220.01910.254723.47668.92871.6108
116.17622.6672-0.74847.3364-4.0822.5295-0.1394-0.3506-0.79220.5212-0.02080.2860.42260.00430.01850.3006-0.02610.06190.14520.04040.29613.53795.20814.8669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 355 through 359 )
2X-RAY DIFFRACTION2chain 'A' and (resid 360 through 366 )
3X-RAY DIFFRACTION3chain 'A' and (resid 367 through 372 )
4X-RAY DIFFRACTION4chain 'A' and (resid 373 through 377 )
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 385 )
6X-RAY DIFFRACTION6chain 'A' and (resid 386 through 393 )
7X-RAY DIFFRACTION7chain 'A' and (resid 394 through 399 )
8X-RAY DIFFRACTION8chain 'A' and (resid 400 through 407 )
9X-RAY DIFFRACTION9chain 'A' and (resid 408 through 416 )
10X-RAY DIFFRACTION10chain 'A' and (resid 417 through 430 )
11X-RAY DIFFRACTION11chain 'A' and (resid 431 through 437 )

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