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- PDB-7bdb: Notum Fragment 916 -

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Basic information

Entry
Database: PDB / ID: 7bdb
TitleNotum Fragment 916
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor Fragment Screen
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway / 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
Chem-NW7 / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: Acs Chem Neurosci / Year: 2022
Title: Structural Analysis and Development of Notum Fragment Screening Hits.
Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / ...Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / Costa, A. / Kjaer, S. / Bictash, M. / Salinas, P.C. / Whiting, P. / Vincent, J.P. / Fish, P.V. / Jones, E.Y.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)44,3907
Polymers43,5671
Non-polymers8236
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-31 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.740, 73.340, 78.450
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
#3: 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: obtained synthetically / 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 , 4 types, 119 molecules

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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NW7 / 3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide


Mass: 235.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.46→59.74 Å / Num. obs: 60338 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 1.46→1.49 Å / Num. unique obs: 2950 / CC1/2: 0.501

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZ1

4uz1


Resolution: 1.46→53.57 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 3039 5.04 %
Rwork0.1963 57232 -
obs0.1971 60271 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.15 Å2 / Biso mean: 24.7256 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 1.46→53.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 50 114 2885
Biso mean--39.57 29.11 -
Num. residues----341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.480.32681190.283825712690100
1.48-1.510.31341240.26782554267899
1.51-1.530.28211360.25482555269199
1.53-1.560.23381230.237725942717100
1.56-1.590.23641320.22082560269299
1.59-1.620.21451300.21632544267499
1.62-1.660.2441220.21012600272299
1.66-1.70.22351180.201425992717100
1.7-1.740.21251250.201525592684100
1.74-1.790.21611260.188726302756100
1.79-1.840.22031510.194425562707100
1.84-1.90.21471590.18922562272199
1.9-1.970.20161470.182925772724100
1.97-2.050.1931360.184826032739100
2.05-2.140.20931620.180725762738100
2.14-2.250.21781430.182726132756100
2.25-2.390.2341310.191926272758100
2.39-2.580.22221420.204826052747100
2.58-2.840.23241380.203326552793100
2.84-3.250.20741520.200326322784100
3.25-4.090.19911360.184227002836100
4.09-53.570.18751870.193427602947100
Refinement TLS params.Method: refined / Origin x: 4.5774 Å / Origin y: -1.0768 Å / Origin z: -2.7558 Å
111213212223313233
T0.1376 Å2-0.0034 Å2-0.0066 Å2-0.1668 Å20.0154 Å2--0.1509 Å2
L0.6931 °20.1208 °2-0.1185 °2-1.1347 °2-0.1349 °2--0.7721 °2
S-0.012 Å °0.0107 Å °0.0492 Å °0.024 Å °-0.0055 Å °-0.0029 Å °-0.083 Å °-0.0045 Å °0.0192 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1501
2X-RAY DIFFRACTION1allC4 - 57
3X-RAY DIFFRACTION1allD8 - 10
4X-RAY DIFFRACTION1allB1

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