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- PDB-7b7w: Notum-Fragment049 -

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Basic information

Entry
Database: PDB / ID: 7b7w
TitleNotum-Fragment049
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Fragment
Function / homology
Function and homology information


protein-containing complex destabilizing activity / [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 ...protein-containing complex destabilizing activity / [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
N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhao, Y. / Jonees, E.Y.
CitationJournal: To Be Published
Title: Notum Fragment Screen
Authors: Zhao, Y. / Jones, E.Y.
History
DepositionDec 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)44,3368
Polymers43,5671
Non-polymers7697
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-15 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.003, 72.680, 78.475
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, 130 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-JGA / N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 4.2 / Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate

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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: 1.6→72.68 Å / Num. obs: 46011 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 1 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 2176 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZQ

4uzq


Resolution: 1.6→53.32 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2168 4.75 %
Rwork0.205 43463 -
obs0.2061 45631 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.47 Å2 / Biso mean: 25.1576 Å2 / Biso min: 12.21 Å2
Refinement stepCycle: final / Resolution: 1.6→53.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 48 124 2920
Biso mean--39.54 31.38 -
Num. residues----351
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 (%)
1.6-1.640.38791370.33022709284694
1.64-1.680.34281370.3212825296298
1.68-1.720.32981270.29982844297199
1.72-1.770.31931430.29182876301999
1.77-1.830.27651370.262228703007100
1.83-1.90.29681410.24882869301099
1.9-1.970.32021520.225528863038100
1.97-2.060.24521430.211528983041100
2.06-2.170.23481390.195228863025100
2.17-2.310.23851340.194929323066100
2.31-2.480.23071540.190928933047100
2.48-2.730.21051500.196129303080100
2.73-3.130.22781610.191829463107100
3.13-3.940.19421470.180129893136100
3.94-53.320.17951660.189231103276100
Refinement TLS params.Method: refined / Origin x: 4.4832 Å / Origin y: -1.1494 Å / Origin z: -2.1492 Å
111213212223313233
T0.1382 Å2-0.001 Å2-0.0078 Å2-0.1618 Å20.0221 Å2--0.15 Å2
L0.7085 °20.0809 °2-0.1125 °2-1.047 °20.0025 °2--0.6223 °2
S-0.0049 Å °-0.0007 Å °0.0668 Å °0.0344 Å °-0.008 Å °0.0162 Å °-0.0821 Å °0.0041 Å °0.0126 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1452
2X-RAY DIFFRACTION1allC4 - 57
3X-RAY DIFFRACTION1allD8
4X-RAY DIFFRACTION1allE2 - 8
5X-RAY DIFFRACTION1allB1

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