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- PDB-7b8u: Notum-Fragment 201 -

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Basic information

Entry
Database: PDB / ID: 7b8u
TitleNotum-Fragment 201
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Fragment
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
4-(piperidin-1-yl)-1,2,5-oxadiazol-3-amine / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsZhao, Y. / Jonees, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Notum Inhibitor
Authors: Zhao, Y. / Jones, E.Y.
History
DepositionDec 13, 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 1.3Nov 6, 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)44,5339
Polymers43,5671
Non-polymers9668
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-73 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 72.758, 79.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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
#4: Chemical ChemComp-RUY / 4-(piperidin-1-yl)-1,2,5-oxadiazol-3-amine


Mass: 168.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 38.33 %
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: 1.54→79.09 Å / Num. obs: 51543 / % possible obs: 98.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 2450 / CC1/2: 0.946

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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: 1.54→53.55 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 2581 5.06 %
Rwork0.2092 48444 -
obs0.2104 51025 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.4 Å2 / Biso mean: 23.112 Å2 / Biso min: 11.89 Å2
Refinement stepCycle: final / Resolution: 1.54→53.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 56 91 2823
Biso mean--40.58 26.36 -
Num. residues----342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.570.34771400.32062548268895
1.57-1.60.34391290.32222631276095
1.6-1.640.32821340.31042563269795
1.64-1.670.3161420.28262625276796
1.67-1.720.30861500.27942639278997
1.72-1.760.31241550.26772622277797
1.76-1.810.27681470.24382647279497
1.82-1.870.28791190.22662677279697
1.87-1.940.2271550.21242636279197
1.94-2.020.23311520.19862654280697
2.02-2.110.22271550.19122684283999
2.11-2.220.21091330.1822729286299
2.22-2.360.19431530.19232715286899
2.36-2.540.21011440.1992731287599
2.54-2.80.22381160.20082795291199
2.8-3.20.22821420.205527872929100
3.2-4.040.24031440.18828272971100
4.04-53.550.19571710.199829343105100
Refinement TLS params.Method: refined / Origin x: 4.7554 Å / Origin y: -1.2293 Å / Origin z: -2.6286 Å
111213212223313233
T0.137 Å20.0018 Å2-0.0003 Å2-0.1501 Å20.0181 Å2--0.1413 Å2
L0.556 °20.1571 °2-0.1016 °2-0.5809 °2-0.0591 °2--0.4412 °2
S-0.0276 Å °0.001 Å °0.0222 Å °0.0197 Å °0.0048 Å °-0.0064 Å °-0.0383 Å °0.0034 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1452
2X-RAY DIFFRACTION1allC4 - 60
3X-RAY DIFFRACTION1allD1 - 11
4X-RAY DIFFRACTION1allB1

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