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- PDB-4uz7: STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VI - 2.2A -

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Basic information

Entry
Database: PDB / ID: 4uz7
TitleSTRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VI - 2.2A
ComponentsPROTEIN 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: 2.2 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1703
Polymers87,1342
Non-polymers351
Water3,729207
1
A: PROTEIN NOTUM HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6032
Polymers43,5671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN NOTUM HOMOLOG


Theoretical massNumber of molelcules
Total (without water)43,5671
Polymers43,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.863, 79.925, 160.004
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21A-2046-

HOH

31B-2038-

HOH

41B-2041-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.001, -0.01), (-0.001, -1, 0.011), (-0.01, -0.011, -1)
Vector: 25.006, -53.643, -80.513)

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Components

#1: Protein PROTEIN NOTUM HOMOLOG


Mass: 43567.148 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 81-451 / Mutation: YES
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) / References: UniProt: Q6P988, carboxylesterase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsC330S ENGINEERED MUTATION

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5
Details: 20 %V/V GLYCEROL 24 %W/V PEG4000 0.160 M MGCL2 0.080 M TRIS-HCL PH 8.5 20MM SOS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→80 Å / Num. obs: 40126 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→79.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.298 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 1063 2.6 %RANDOM
Rwork0.18271 ---
obs0.18397 39061 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.807 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å2-0.64 Å2
2---1.52 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→79.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 1 207 5908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195886
X-RAY DIFFRACTIONr_bond_other_d0.0010.025411
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.948017
X-RAY DIFFRACTIONr_angle_other_deg0.819312414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75822.482282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71915933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0991558
X-RAY DIFFRACTIONr_chiral_restr0.0850.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021469
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_it1.7512.6422861
X-RAY DIFFRACTIONr_mcbond_other1.7462.6412860
X-RAY DIFFRACTIONr_mcangle_it2.8663.9493569
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.462.9943025
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 78 -
Rwork0.263 2888 -
obs--99.83 %
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)
10.39140.06660.04950.45440.0710.5174-0.0475-0.00250.0162-0.06310.04920.0049-0.0098-0.0513-0.00180.0188-0.0137-0.00580.06550.01180.0038-14.5568-25.8751-19.8335
20.3322-0.00960.18970.91980.080.4203-0.0166-0.0305-0.01090.0760.02860.10770.0031-0.0387-0.0120.00770.00560.01010.06420.00770.0156-40.1477-28.6527-60.1201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A87 - 451
2X-RAY DIFFRACTION2B87 - 451

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