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- PDB-7bcc: Notum Fragment 705 -

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Basic information

Entry
Database: PDB / ID: 7bcc
TitleNotum Fragment 705
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 / 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-(4-pyrrol-1-ylphenyl)morpholine / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 19, 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)44,4978
Polymers43,5671
Non-polymers9307
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-62 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.470, 72.505, 78.874
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / 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 / 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
#4: Chemical ChemComp-TB5 / 4-(4-pyrrol-1-ylphenyl)morpholine / 4-[4-(1H-pyrrol-1-yl)phenyl]morpholine


Mass: 228.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 38.02 %
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: 1.58→78.87 Å / Num. obs: 48153 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 9.2
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 2327 / CC1/2: 0.7

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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→53.38 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2326 4.87 %
Rwork0.2177 45392 -
obs0.2185 47718 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.45 Å2 / Biso mean: 25.0381 Å2 / Biso min: 13.39 Å2
Refinement stepCycle: final / Resolution: 1.58→53.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 56 92 2949
Biso mean--38.1 28.57 -
Num. residues----352
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 (%)
1.58-1.610.39631260.35132571269797
1.61-1.650.36251370.32312615275298
1.65-1.690.31611340.31072651278599
1.69-1.730.37421430.29972582272599
1.73-1.770.34131370.27542620275798
1.77-1.830.31751400.25942636277699
1.83-1.890.30031280.24892626275498
1.89-1.950.27741170.23112677279499
1.95-2.030.26811090.21562656276599
2.03-2.120.21821380.210226752813100
2.12-2.240.20671350.197726782813100
2.24-2.380.23821410.201526822823100
2.38-2.560.22821380.20692689282799
2.56-2.820.21221340.214627052839100
2.82-3.220.21261550.212727062861100
3.23-4.060.21911410.198527532894100
4.06-53.380.20481730.200728703043100
Refinement TLS params.Method: refined / Origin x: 4.46 Å / Origin y: -1.241 Å / Origin z: -1.948 Å
111213212223313233
T0.1435 Å2-0.0004 Å2-0.0128 Å2-0.172 Å20.0201 Å2--0.1606 Å2
L0.8229 °20.144 °2-0.2931 °2-1.2779 °20.1021 °2--0.9805 °2
S-0.0195 Å °0.0281 Å °0.0256 Å °0.0053 Å °0.0037 Å °-0.0122 Å °-0.0822 Å °0.0178 Å °0.0123 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A88 - 451
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A501 - 502
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A604 - 692
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A601 - 603
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A507
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 88:451 OR RESID 501:502 OR RESID 604:692 OR RESID 601:603 OR RESID 507:507 OR RESID 503:506 ) )A503 - 506

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