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- PDB-4uzj: STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA - CRYSTAL FO... -

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Basic information

Entry
Database: PDB / ID: 4uzj
TitleSTRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA - CRYSTAL FORM I - 2.4A
ComponentsNOTUM
KeywordsHYDROLASE / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


GPI anchor release / regulation of compound eye pigmentation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Release of Hh-Np from the secreting cell / wing disc dorsal/ventral pattern formation / wing disc pattern formation / wing disc development / ventral cord development / [Wnt protein] O-palmitoleoyl-L-serine hydrolase ...GPI anchor release / regulation of compound eye pigmentation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Release of Hh-Np from the secreting cell / wing disc dorsal/ventral pattern formation / wing disc pattern formation / wing disc development / ventral cord development / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / positive regulation of smoothened signaling pathway / digestive tract morphogenesis / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / cell surface / extracellular space
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: Nature / Year: 2015
Title: Notum Deacylates Wnt Proteins to Suppress Signalling Activity.
Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J.
History
DepositionSep 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Structure summary
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Other
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NOTUM
B: NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1013
Polymers84,8802
Non-polymers2211
Water25214
1
A: NOTUM


Theoretical massNumber of molelcules
Total (without water)42,4401
Polymers42,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6612
Polymers42,4401
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.388, 81.394, 86.945
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.01, -0.011), (0.002, -0.829, 0.56), (-0.015, 0.56, 0.829)
Vector: -25.597, -32.527, 9.405)

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Components

#1: Protein NOTUM / NOTUM PROTEIN / WINGFUL


Mass: 42439.934 Da / Num. of mol.: 2 / Fragment: RESIDUES 82-415,598-617
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED AT N95 / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q9VUX3, carboxylesterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsR416-K597 REPLACED BY GNNNG LINKER

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.5
Details: 0.12 M ALCOHOLS, 0.1 M TRIS/BICINE 8.5, 30 % EDO_P8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→58 Å / Num. obs: 30929 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→83.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 21.748 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24338 1030 3.3 %RANDOM
Rwork0.19685 ---
obs0.19842 29879 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å23.07 Å2
2---3.79 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→83.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 14 14 5497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195659
X-RAY DIFFRACTIONr_bond_other_d0.0010.025238
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9357701
X-RAY DIFFRACTIONr_angle_other_deg0.813312013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9922.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44815906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.031554
X-RAY DIFFRACTIONr_chiral_restr0.0840.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021412
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3553.6462718
X-RAY DIFFRACTIONr_mcbond_other2.3543.6452717
X-RAY DIFFRACTIONr_mcangle_it3.7415.4613387
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0314.0142941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 82 -
Rwork0.323 2184 -
obs--99.43 %
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)
12.0332-0.35610.15020.9626-1.17021.4697-0.03230.0504-0.0237-0.2342-0.0017-0.00170.30970.01530.0340.21620.0402-0.09140.46290.01850.1085-22.6478-31.497525.3906
22.22941.10940.41031.078-0.31910.8019-0.1059-0.17090.0217-0.03490.07050.0982-0.19050.00640.03540.16590.0309-0.10430.53040.02710.0881-2.8447.537813.1459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B85 - 1617
2X-RAY DIFFRACTION2A84 - 617

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