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- PDB-4uz5: STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A -

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Basic information

Entry
Database: PDB / ID: 4uz5
TitleSTRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A
ComponentsNOTUM
KeywordsHYDROLASE / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE
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
Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: Nature / Year: 2015
Title: Notum Deacylates Wnt Proteins to Suppress Signalling Activity.
Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J.
History
DepositionSep 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8243
Polymers43,5671
Non-polymers2572
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.416, 138.416, 138.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

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Components

#1: Protein NOTUM


Mass: 43567.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-452 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED AT N96 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6P988, carboxylesterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6
Details: 10 %W/V PEG4000, 0.01 M CACL2, 0.05 M NACACOD PH 6.0, 0.20 M KCL, 1 MM HEPARIN HEXAMER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→69 Å / Num. obs: 27077 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→97.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.873 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1046 3.9 %RANDOM
Rwork0.18746 ---
obs0.18936 25980 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.492 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 15 84 2895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192902
X-RAY DIFFRACTIONr_bond_other_d0.0010.022663
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9433956
X-RAY DIFFRACTIONr_angle_other_deg0.81736099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15222.553141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0331529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2663.2311397
X-RAY DIFFRACTIONr_mcbond_other2.2573.2281396
X-RAY DIFFRACTIONr_mcangle_it3.3984.8281742
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.383.7321505
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 73 -
Rwork0.272 1868 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: -21.6694 Å / Origin y: 18.0125 Å / Origin z: -13.3796 Å
111213212223313233
T0.008 Å20.0067 Å2-0.011 Å2-0.0608 Å20.0218 Å2--0.0454 Å2
L1.1714 °20.4021 °2-0.2091 °2-0.7453 °2-0.1657 °2--0.6822 °2
S-0.0424 Å °0.0265 Å °0.0182 Å °-0.0528 Å °-0.0012 Å °0.0869 Å °0.0396 Å °0.1118 Å °0.0437 Å °

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