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- PDB-1at0: 17-kDA fragment of hedgehog C-terminal autoprocessing domain -

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Basic information

Entry
Database: PDB / ID: 1at0
Title17-kDA fragment of hedgehog C-terminal autoprocessing domain
Components17-HEDGEHOG
KeywordsSIGNALING PROTEIN / DEVELOPMENTAL SIGNALING MOLECULE / CHOLESTEROL TRANSFER
Function / homology
Function and homology information


progression of morphogenetic furrow involved in compound eye morphogenesis / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell / Ligand-receptor interactions ...progression of morphogenetic furrow involved in compound eye morphogenesis / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell / Ligand-receptor interactions / leg disc morphogenesis / Formation and transport of the N-HH ligand / regulation of epithelial cell migration, open tracheal system / morphogenesis of larval imaginal disc epithelium / cell-cell signaling involved in cell fate commitment / Assembly of the 'signalling complexes' / gonadal mesoderm development / compound eye photoreceptor cell differentiation / wing disc pattern formation / negative regulation of homotypic cell-cell adhesion / Hedgehog ligand biogenesis / imaginal disc growth / : / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / epithelial cell migration, open tracheal system / trunk segmentation / heart formation / genital disc development / genital disc anterior/posterior pattern formation / compound eye morphogenesis / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / morphogen activity / mucosal immune response / hindgut morphogenesis / segment polarity determination / ventral midline development / foregut morphogenesis / cholesterol-protein transferase activity / imaginal disc-derived wing morphogenesis / compartment pattern specification / glial cell migration / developmental pigmentation / patched binding / germ cell migration / self proteolysis / embryonic pattern specification / positive regulation of protein localization to cell surface / intein-mediated protein splicing / cell fate specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / regulation of mitotic cell cycle / protein autoprocessing / endocytic vesicle / epidermis development / negative regulation of proteolysis / heart development / peptidase activity / cytoplasmic vesicle / regulation of gene expression / Hydrolases; Acting on ester bonds / endosome / calcium ion binding / extracellular space / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHall, T.M.T. / Porter, J.A. / Young, K.E. / Koonin, E.V. / Beachy, P.A. / Leahy, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins.
Authors: Hall, T.M. / Porter, J.A. / Young, K.E. / Koonin, E.V. / Beachy, P.A. / Leahy, D.J.
History
DepositionAug 15, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Other / Refinement description / Category: pdbx_database_status / refine
Item: _pdbx_database_status.process_site / _refine.pdbx_method_to_determine_struct

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17-HEDGEHOG


Theoretical massNumber of molelcules
Total (without water)15,9861
Polymers15,9861
Non-polymers00
Water2,270126
1
A: 17-HEDGEHOG

A: 17-HEDGEHOG


Theoretical massNumber of molelcules
Total (without water)31,9722
Polymers31,9722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
Unit cell
Length a, b, c (Å)101.540, 101.540, 101.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein 17-HEDGEHOG


Mass: 15985.778 Da / Num. of mol.: 1 / Fragment: 17-KDA FRAGMENT OF C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line: B834 / Plasmid: PRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: Q02936
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.73 Å3/Da / Density % sol: 59 %
Description: DATA WERE COLLECTED AT 0.9919, 0.9793, 0.9791, AND 0.9686 ANGSTROM. VALUES FOR DATA COLLECTION AND DATA QUALITY ARE FOR 0.9919.
Crystal growpH: 5.8
Details: 20% PEG 3350, 80 mM AMMONIUM SULFATE, 10 mM SODIUM CACODYLATE pH 5.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 mg/mlHh-C171drop
21.4 mMbeta-mercaptoethanol1drop
320 %PEG33501reservoir
480 mMammonium sulfate1reservoir
510 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9919
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 26790 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rsym value: 0.092 / Net I/σ(I): 19.9
Reflection shellResolution: 1.9→1.98 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.529 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å / Rfactor Rfree error: 0.0077 / Cross valid method: ALL BUT LAST ROUND / σ(F): 2 / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1289 10 %RANDOM
Rwork0.2176 ---
obs0.2176 13163 100 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 126 1870
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.956
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.38
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.135
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.0721.5
X-RAY DIFFRACTIONx_mcangle_it32
X-RAY DIFFRACTIONx_scbond_it4.3542
X-RAY DIFFRACTIONx_scangle_it6.5322.5
LS refinement shellResolution: 1.9→1.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3155 150 9.915 %
Rwork0.2932 1277 -
obs--96.75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX_MOD.PROTOPHCSDX_SE.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.ION
X-RAY DIFFRACTION3PARAM19.IONTOPH19.SOL
X-RAY DIFFRACTION4PARAM19X.SE
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2754
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.382
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.135
LS refinement shell
*PLUS
% reflection Rfree: 9.9159 %

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