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- PDB-6tr6: N-acetylserotonin-Notum complex -

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Basic information

Entry
Database: PDB / ID: 6tr6
TitleN-acetylserotonin-Notum complex
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsONCOPROTEIN / Wnt Notum inhibitor
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
N-ACETYL SEROTONIN / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: J. Pineal Res. / Year: 2020
Title: Structural characterization of melatonin as an inhibitor of the Wnt deacylase Notum.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Jones, M. / Lu, W. / Jones, E.Y.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,04614
Polymers43,5671
Non-polymers1,47913
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-23 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.510, 72.730, 77.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Palmitoleoyl-protein carboxylesterase NOTUM / hNOTUM


Mass: 43567.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human)
References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


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

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Non-polymers , 5 types, 164 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ASE / N-ACETYL SEROTONIN / N-Acetylserotonin


Mass: 218.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.5 M ammonium sulphate 0.1 M sodium citrate pH 4.2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.04 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.35→72.73 Å / Num. obs: 72849 / % possible obs: 97.4 % / Redundancy: 10.9 % / CC1/2: 1 / Net I/σ(I): 23.3
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 2717 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZQ

4uzq


Resolution: 1.35→39.64 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.1928 3668 5.04 %
Rwork0.1806 --
obs0.1812 72767 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.27 Å2 / Biso mean: 23.9797 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.35→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 90 152 3014
Biso mean--42.64 29.25 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.36780.35551020.3099195473
1.3678-1.38650.35481060.2873216280
1.3865-1.40630.34311250.2774232887
1.4063-1.42730.25131450.2513249993
1.4273-1.44960.27171420.2319263497
1.4496-1.47340.23571440.21812681100
1.4734-1.49880.23641410.20342723100
1.4988-1.52610.20621450.18752717100
1.5261-1.55540.19311420.1762677100
1.5554-1.58720.19261380.17392727100
1.5872-1.62170.18861310.16632712100
1.6217-1.65940.21771480.17172712100
1.6594-1.70090.17251260.16652731100
1.7009-1.74690.20071420.16572706100
1.7469-1.79830.1741400.16482715100
1.7983-1.85630.1741540.17082727100
1.8563-1.92270.18551390.16472715100
1.9227-1.99970.1581190.16412765100
1.9997-2.09070.16161760.16162700100
2.0907-2.20090.1691640.15872703100
2.2009-2.33880.18781380.17212750100
2.3388-2.51930.18671580.17522752100
2.5193-2.77280.18321550.18352757100
2.7728-3.17390.20171430.18722788100
3.1739-3.99810.18481420.17372825100
Refinement TLS params.Method: refined / Origin x: 4.5552 Å / Origin y: -1.1034 Å / Origin z: -2.8722 Å
111213212223313233
T0.1394 Å2-0.0029 Å2-0.0017 Å2-0.1468 Å20.0134 Å2--0.1372 Å2
L0.6067 °20.11 °2-0.025 °2-0.6505 °2-0.0125 °2--0.471 °2
S-0.0184 Å °-0.0112 Å °0.0216 Å °0.016 Å °0.0041 Å °0.0271 Å °-0.0615 Å °-0.0003 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 451
2X-RAY DIFFRACTION1allA462 - 780
3X-RAY DIFFRACTION1allB1 - 2
4X-RAY DIFFRACTION1allC1 - 2

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