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- PDB-7b8f: Notum-Fragment 154 -

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Basic information

Entry
Database: PDB / ID: 7b8f
TitleNotum-Fragment 154
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 / 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
4-(benzimidazol-1-ylmethyl)benzenecarbonitrile / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 1.3Nov 20, 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)44,59210
Polymers43,5671
Non-polymers1,0259
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-42 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.817, 72.946, 78.566
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, 143 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-RYM / 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile


Mass: 233.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
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: 1.62→72.95 Å / Num. obs: 43862 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 11.5
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 2067 / CC1/2: 0.581

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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: 1.62→53.46 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 2127 4.89 %
Rwork0.2058 41333 -
obs0.2073 43460 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.21 Å2 / Biso mean: 27.2112 Å2 / Biso min: 12.3 Å2
Refinement stepCycle: final / Resolution: 1.62→53.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 64 135 2943
Biso mean--45.28 32.96 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.660.41961230.36572580270393
1.66-1.70.36871440.35452648279296
1.7-1.750.32871350.32262680281596
1.75-1.80.3431490.29622671282097
1.8-1.850.28621720.27782678285098
1.85-1.920.28441430.24842726286997
1.92-20.27881350.21672725286098
2-2.090.24371370.19422741287899
2.09-2.20.20771540.18142766292099
2.2-2.340.231290.18442783291299
2.34-2.520.25161370.18632810294799
2.52-2.770.22051530.19882789294299
2.77-3.170.21931540.19232827298199
3.17-3.990.20751370.182728823019100
4-53.460.20511250.193830273152100
Refinement TLS params.Method: refined / Origin x: 4.4589 Å / Origin y: -1.3509 Å / Origin z: -2.5767 Å
111213212223313233
T0.0653 Å20.0011 Å20.0004 Å2-0.0766 Å20.0149 Å2--0.0708 Å2
L0.263 °20.1202 °2-0.0808 °2-0.3992 °2-0.1305 °2--0.2736 °2
S-0.0216 Å °0.0141 Å °0.0016 Å °0.0084 Å °-0.0048 Å °0.0063 Å °-0.0514 Å °-0.0009 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1452
2X-RAY DIFFRACTION1allC4 - 58
3X-RAY DIFFRACTION1allD1 - 9
4X-RAY DIFFRACTION1allE3 - 7
5X-RAY DIFFRACTION1allB1

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