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- PDB-7b9n: Notum Fragment 588 -

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Basic information

Entry
Database: PDB / ID: 7b9n
TitleNotum Fragment 588
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor
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 / negative regulation of canonical Wnt signaling pathway / bone development ...[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 / 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
benzyl hydroxycarbamate / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 14, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)44,93313
Polymers43,5671
Non-polymers1,36612
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-63 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.016, 73.227, 78.740
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


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, 123 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-N9J / benzyl hydroxycarbamate


Mass: 167.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.06 %
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: 1.38→78.74 Å / Num. obs: 71450 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 1.38→1.4 Å / Num. unique obs: 3475 / CC1/2: 0.463

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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: 4UZQ

4uzq


Resolution: 1.38→53.62 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 3483 4.87 %
Rwork0.2038 67967 -
obs0.205 71450 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.08 Å2 / Biso mean: 21.8929 Å2 / Biso min: 10.24 Å2
Refinement stepCycle: final / Resolution: 1.38→53.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 80 112 2880
Biso mean--37.19 27.1 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.40.35871200.35712531265193
1.4-1.420.39381170.3552620273797
1.42-1.440.37811180.35022675279398
1.44-1.460.34891370.34652673281098
1.46-1.490.39541400.32262683282399
1.49-1.510.33591410.29762678281999
1.51-1.540.33511460.29412682282899
1.54-1.570.29081450.26426792824100
1.57-1.60.29671400.25127222862100
1.6-1.640.25311280.24642719284799
1.64-1.670.33541130.23272724283799
1.67-1.720.2661440.224127162860100
1.72-1.760.22231610.211426782839100
1.76-1.810.23291440.204427072851100
1.81-1.870.22551450.192527322877100
1.87-1.940.19671440.185727042848100
1.94-2.020.21041270.177627582885100
2.02-2.110.23741580.173127142872100
2.11-2.220.18521440.171827242868100
2.22-2.360.2011350.183227672902100
2.36-2.540.20591420.183627462888100
2.54-2.80.20431510.192227702921100
2.8-3.20.21771690.195627602929100
3.2-4.030.20211340.18428382972100
4.03-53.620.21891400.196629673107100
Refinement TLS params.Method: refined / Origin x: 4.437 Å / Origin y: -1.1831 Å / Origin z: -2.746 Å
111213212223313233
T0.0998 Å20.0018 Å2-0.0071 Å2-0.1226 Å20.0147 Å2--0.1067 Å2
L0.6036 °20.1147 °2-0.1578 °2-0.9872 °2-0.0481 °2--0.8005 °2
S-0.0278 Å °0.0088 Å °0.0133 Å °0.0147 Å °0.002 Å °-0.0051 Å °-0.0608 Å °0.009 Å °0.0244 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA89 - 1701
2X-RAY DIFFRACTION1allC4 - 50
3X-RAY DIFFRACTION1allD1 - 12
4X-RAY DIFFRACTION1allB1 - 2

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