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- PDB-7b87: Notum-Fragment074 -

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Basic information

Entry
Database: PDB / ID: 7b87
TitleNotum-Fragment074
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
methyl 2-(4-aminophenoxy)benzoate / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZhao, Y. / Jonees, 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 12, 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 9, 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)44,91115
Polymers43,5671
Non-polymers1,34314
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-1 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 73.162, 78.671
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
#5: 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 , 5 types, 131 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-JFV / methyl 2-(4-aminophenoxy)benzoate


Mass: 243.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.98 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 296 K / Method: evaporation
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: 1.58→73.16 Å / Num. obs: 47981 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 6.8
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 2329 / CC1/2: 0.536

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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: 1.58→53.58 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 2327 4.89 %
Rwork0.221 45282 -
obs0.2221 47609 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.59 Å2 / Biso mean: 23.5545 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 1.58→53.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 83 118 2967
Biso mean--39.31 28.46 -
Num. residues----344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.610.32851290.35382544267396
1.61-1.650.37311300.34862587271797
1.65-1.690.39671330.33692622275599
1.69-1.730.35141400.32642599273999
1.73-1.770.35791470.30352602274999
1.77-1.830.33281430.29492650279399
1.83-1.890.28051220.26772632275499
1.89-1.950.27551120.248126752787100
1.95-2.030.24851140.22782662277699
2.03-2.120.22361370.218726462783100
2.12-2.240.24671410.205326852826100
2.24-2.380.28321380.212626732811100
2.38-2.560.23161350.208126992834100
2.56-2.820.19541380.211627082846100
2.82-3.220.21141570.199126852842100
3.22-4.060.21241370.183127562893100
4.06-53.580.21291740.197128573031100
Refinement TLS params.Method: refined / Origin x: 4.5832 Å / Origin y: -1.3677 Å / Origin z: -2.6569 Å
111213212223313233
T0.1329 Å2-0.0031 Å2-0.0065 Å2-0.1528 Å20.011 Å2--0.1403 Å2
L0.6194 °20.0885 °2-0.0463 °2-0.9339 °2-0.0826 °2--0.6579 °2
S-0.0105 Å °-0.0116 Å °0.0286 Å °0.0272 Å °0.0069 Å °-0.0013 Å °-0.0732 Å °0.0078 Å °0.006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1501
2X-RAY DIFFRACTION1allB1

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