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- PDB-4uyz: STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A -

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Basic information

Entry
Database: PDB / ID: 4uyz
TitleSTRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A
Components
  • POLY ALA
  • PROTEIN NOTUM HOMOLOG
KeywordsHYDROLASE / WNT / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE
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
Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 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 3, 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: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN NOTUM HOMOLOG
B: PROTEIN NOTUM HOMOLOG
C: PROTEIN NOTUM HOMOLOG
D: PROTEIN NOTUM HOMOLOG
E: POLY ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,3817
Polymers213,1245
Non-polymers2572
Water00
1
A: PROTEIN NOTUM HOMOLOG


Theoretical massNumber of molelcules
Total (without water)53,0991
Polymers53,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN NOTUM HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3563
Polymers53,0991
Non-polymers2572
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN NOTUM HOMOLOG


Theoretical massNumber of molelcules
Total (without water)53,0991
Polymers53,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROTEIN NOTUM HOMOLOG


Theoretical massNumber of molelcules
Total (without water)53,0991
Polymers53,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: POLY ALA


  • defined by author&software
  • 729 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7291
Polymers7291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.829, 193.880, 75.717
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.003, -0.015), (0.011, 0.586, -0.81), (0.011, -0.81, -0.586)92.845, 11.69, 24.687
2given(-0.998, 0.045, -0.043), (-0.061, -0.587, 0.808), (0.011, 0.809, 0.588)93.58, -7.968, -6.55
3given(0.996, 0.061, -0.058), (0.061, -0.998, 0.01), (-0.057, -0.013, -0.998)-3.823, 8.518, 40.674

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Components

#1: Protein
PROTEIN NOTUM HOMOLOG / NOTUM


Mass: 53098.891 Da / Num. of mol.: 4 / Fragment: RESIDUES 38-496
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: Protein/peptide POLY ALA


Mass: 728.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
#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: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 2.09 Å3/Da / Density % sol: 41.26 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.02
DetectorDate: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.8→58 Å / Num. obs: 38300 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.6

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Processing

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

Resolution: 2.8→96.94 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.851 / SU B: 52.567 / SU ML: 0.443 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29294 1143 3 %RANDOM
Rwork0.24761 ---
obs0.24899 37125 88.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.978 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å2-0.06 Å2
2---3.92 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→96.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10976 0 15 0 10991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.94115399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89651379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21822.337522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49151732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.06615110
X-RAY DIFFRACTIONr_chiral_restr0.0860.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218726
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9162.1745567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6493.2536929
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1352.275737
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 77 -
Rwork0.369 2549 -
obs--83.68 %
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)
11.44550.35660.16450.5150.70651.9008-0.1113-0.0530.0802-0.16890.0477-0.03-0.1483-0.02060.06370.0787-0.01680.01070.5262-0.05190.042263.0104-27.18639.2323
20.7177-0.22260.05961.24750.81261.50710.00570.0463-0.15310.0803-0.0915-0.016-0.1331-0.0290.08580.0456-0.0005-0.03610.6676-0.08990.069729.6177-10.442941.7262
31.5376-0.17160.43870.85920.29881.498-0.09770.042-0.17350.24570.1755-0.11320.0105-0.0526-0.07780.07490.0669-0.02740.5431-0.03730.041164.46338.098928.875
40.66940.22180.46291.72760.76541.2005-0.0259-0.05180.1062-0.1061-0.11330.00930.027-0.04130.13920.01730.02890.00390.594-0.09460.040232.275420.2252-2.1352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 451
2X-RAY DIFFRACTION2A87 - 452
3X-RAY DIFFRACTION3C87 - 450
4X-RAY DIFFRACTION4D87 - 472

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