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- PDB-6tuz: Theophylline-Notum complex -

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Basic information

Entry
Database: PDB / ID: 6tuz
TitleTheophylline-Notum complex
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsSIGNALING PROTEIN / Wnt Notum inhibitor complex
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
THEOPHYLLINE / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: Commun Biol / Year: 2020
Title: Caffeine inhibits Notum activity by binding at the catalytic pocket.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 1.2Oct 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)46,00332
Polymers43,5671
Non-polymers2,43631
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint23 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.425, 73.141, 78.880
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 / Cell line (production host): HEK293S GNTI- / 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: isolated from a genetically manipulated source
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, 207 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H8N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.2 / 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: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.24→78.88 Å / Num. obs: 1189310 / % possible obs: 99.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 11.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 4742 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
PHENIXv1.3refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R8P

6r8p


Resolution: 1.24→53.633 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2167 9798 5.18 %
Rwork0.2013 --
obs0.2021 189310 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.34 Å2 / Biso mean: 21.2903 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: final / Resolution: 1.24→53.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 148 177 3135
Biso mean--39.92 28.38 -
Num. residues----351
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78130.1193-0.08811.09320.20381.1367-0.0208-0.00170.11530.0160.0065-0.0218-0.15970.04020.01350.1178-0.006-0.01350.08680.01210.11617.586310.4751-0.61
20.9203-0.1411-0.09661.805-0.39240.3511-0.0252-0.02880.01120.0750.0450.1243-0.0948-0.0474-0.03870.0850.00350.00310.10070.00880.0985-0.3718-1.8406-3.0194
31.69430.98690.68461.81441.2421.34040.049-0.17850.18330.0876-0.1150.2275-0.0475-0.15840.02960.1124-0.00160.0290.1547-0.00480.1534-10.6792-1.98934.6755
40.50570.0268-0.11920.5627-0.07840.3336-0.0171-0.0083-0.0573-0.0164-0.0007-0.03950.02580.01740.03190.0981-0.0020.00450.12040.00820.11136.9461-11.3638-4.7999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 224 )A87 - 224
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 286 )A225 - 286
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 320 )A287 - 320
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 454 )A321 - 454

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