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- PDB-3odn: The crystal structure of Drosophila Dally-Like Protein core domain -

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Basic information

Entry
Database: PDB / ID: 3odn
TitleThe crystal structure of Drosophila Dally-Like Protein core domain
ComponentsDally-like protein
KeywordsMEMBRANE PROTEIN / alpha Helical bundle / Hedgehog signaling / Hedgehog via Co-Immunoprecipitation
Function / homology
Function and homology information


perivitelline space / Signaling by ROBO receptors / Formation and transport of the N-HH ligand / cytoneme / regulation of imaginal disc growth / imaginal disc-derived wing margin morphogenesis / regulation of protein localization to membrane / HS-GAG biosynthesis / HS-GAG degradation / Assembly of the 'signalling complexes' ...perivitelline space / Signaling by ROBO receptors / Formation and transport of the N-HH ligand / cytoneme / regulation of imaginal disc growth / imaginal disc-derived wing margin morphogenesis / regulation of protein localization to membrane / HS-GAG biosynthesis / HS-GAG degradation / Assembly of the 'signalling complexes' / wing disc dorsal/ventral pattern formation / A tetrasaccharide linker sequence is required for GAG synthesis / epithelial cell migration, open tracheal system / segment polarity determination / compound eye development / hedgehog family protein binding / segment specification / positive regulation of fibroblast growth factor receptor signaling pathway / Wnt-protein binding / positive regulation of smoothened signaling pathway / neuromuscular junction development / positive regulation of Wnt signaling pathway / regulation of signal transduction / side of membrane / axon guidance / neuromuscular junction / positive regulation of canonical Wnt signaling pathway / cell migration / : / axon / external side of plasma membrane / synapse / cell surface / plasma membrane
Similarity search - Function
Dally-like protein / Dally-like, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKim, M.-S. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the protein core of the glypican Dally-like and localization of a region important for hedgehog signaling.
Authors: Kim, M.S. / Saunders, A.M. / Hamaoka, B.Y. / Beachy, P.A. / Leahy, D.J.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dally-like protein


Theoretical massNumber of molelcules
Total (without water)57,6511
Polymers57,6511
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.021, 66.424, 85.725
Angle α, β, γ (deg.)90.00, 104.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dally-like protein


Mass: 57650.551 Da / Num. of mol.: 1 / Fragment: UNP residues 74-399, 438-617 / Mutation: N79E, N502E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dlp, CG32146 / Plasmid: pSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9GPL5, UniProt: Q9VUG1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.7
Details: 20% PEG 3350, 0.2M Mg formate, pH 6.7, EVAPORATION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 20563 / Biso Wilson estimate: 59.41 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→28.28 Å / Cor.coef. Fo:Fc: 0.9158 / Cor.coef. Fo:Fc free: 0.8845 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 1054 5.13 %RANDOM
Rwork0.2469 ---
obs0.2495 20563 --
Displacement parametersBiso mean: 79.46 Å2
Baniso -1Baniso -2Baniso -3
1--4.8529 Å20 Å28.9834 Å2
2---4.001 Å20 Å2
3---8.8539 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 0 69 3003
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0129932
X-RAY DIFFRACTIONt_angle_deg1.1540302
X-RAY DIFFRACTIONt_dihedral_angle_d10662
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes812
X-RAY DIFFRACTIONt_gen_planes4285
X-RAY DIFFRACTIONt_it299320
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion21.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3915
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact34604
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 166 5.52 %
Rwork0.2721 2842 -
all0.273 3008 -
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)
1-0.1254-0.68720.49040.0088-0.78110.5886-0.0052-0.02880.01940.0625-0.02710.0629-0.0197-0.02920.0323-0.13540.0836-0.16950.20640.1696-0.122212.114965.9117-9.5486
21.9366-0.83141.31391.6256-2.71549.07780.01720.1069-0.1833-0.0550.3570.40010.5929-0.401-0.3742-0.0336-0.0735-0.1095-0.23640.0402-0.263149.438348.394234.3086
3-0.0301-0.83990.8611.5042-2.27778.69910.0787-0.0429-0.13840.21210.19260.1465-0.4991-0.2695-0.2713-0.12560.0101-0.0601-0.20550.0353-0.345250.006458.250123.8548
43.4197-1.73853.09312.5764-1.33154.32250.1311-0.01970.1262-0.1799-0.25660.1893-0.5575-0.41970.12540.10330.1525-0.0223-0.07810.018-0.344138.384470.45517.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - A128A117 - 128
2X-RAY DIFFRACTION2A129 - A227A129 - 227
3X-RAY DIFFRACTION3A228 - A547A228 - 547
4X-RAY DIFFRACTION4A548 - A614A548 - 614

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