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- PDB-7el5: Crystal structure of Sizzled protein from Xenopus Laevis -

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Basic information

Entry
Database: PDB / ID: 7el5
TitleCrystal structure of Sizzled protein from Xenopus Laevis
ComponentsSecreted Xwnt8 inhibitor sizzled
KeywordsSIGNALING PROTEIN / BMP1-inhibitor / Sizzled / Wnt signaling / Frizzled motif
Function / homology
Function and homology information


G protein-coupled receptor activity / plasma membrane
Similarity search - Function
Sizzled, cysteine-rich domain / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Netrin domain / NTR domain profile.
Similarity search - Domain/homology
Secreted Xwnt8 inhibitor sizzled
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSharma, U. / Harlos, K. / Hulmes, D.J.S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)2010-BLAN-1526-01 France
CitationJournal: Sci Rep / Year: 2022
Title: Dynamics of the secreted frizzled related protein Sizzled and potential implications for binding to bone morphogenetic protein-1 (BMP-1).
Authors: Sharma, U. / Vadon-Le Goff, S. / Harlos, K. / Zhao, Y. / Mariano, N. / Bijakowski, C. / Bourhis, J.M. / Moali, C. / Hulmes, D.J.S. / Aghajari, N.
History
DepositionApr 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted Xwnt8 inhibitor sizzled
B: Secreted Xwnt8 inhibitor sizzled


Theoretical massNumber of molelcules
Total (without water)62,9592
Polymers62,9592
Non-polymers00
Water2,234124
1
A: Secreted Xwnt8 inhibitor sizzled


Theoretical massNumber of molelcules
Total (without water)31,4791
Polymers31,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted Xwnt8 inhibitor sizzled


Theoretical massNumber of molelcules
Total (without water)31,4791
Polymers31,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.880, 77.480, 107.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Secreted Xwnt8 inhibitor sizzled


Mass: 31479.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: szl.S, szl / Plasmid: pHLSec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Strain (production host): Human / References: UniProt: O73821
#2: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M NH4Ac, 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→19.91 Å / Num. obs: 74377 / % possible obs: 98.9 % / Redundancy: 13.7 % / CC1/2: 0.83 / Net I/σ(I): 15.58
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 5413 / CC1/2: 0.825 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 3726 5 %
Rwork0.205 70606 -
obs0.207 74332 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.73 Å2 / Biso mean: 45.6 Å2 / Biso min: 25.12 Å2
Refinement stepCycle: final / Resolution: 1.95→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 0 124 3874
Biso mean---44.14 -
Num. residues----476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.970.3621370.315260298
1.97-20.341380.318259598
2-2.030.3181380.304259498
2.03-2.060.3591370.266260399
2.06-2.090.3251340.256258099
2.09-2.120.3041370.238262798
2.12-2.150.2651350.237258198
2.15-2.190.2371390.226262799
2.19-2.230.2531370.225260999
2.23-2.270.2441360.215262699
2.27-2.320.2951330.224257199
2.32-2.370.2321400.217264199
2.37-2.430.231330.227259699
2.43-2.490.2661420.214261899
2.49-2.550.2461400.218261999
2.55-2.630.2441400.224259199
2.63-2.710.2631400.226263699
2.71-2.810.2461420.223261399
2.81-2.920.2851380.216260299
2.92-3.060.2541390.2242658100
3.06-3.220.2361390.216263099
3.22-3.420.2361370.2142613100
3.42-3.680.2571420.1932661100
3.68-4.050.2621340.1792599100
4.05-4.620.2011380.1752654100
4.63-5.80.1991410.182635100
5.8-19.910.2131400.185262599
Refinement TLS params.Method: refined / Origin x: 49.0819 Å / Origin y: 13.8529 Å / Origin z: 41.8238 Å
111213212223313233
T0.229 Å20.025 Å2-0.0175 Å2-0.3211 Å20.0044 Å2--0.2911 Å2
L0.1486 °20.0367 °2-0.0226 °2-2.0243 °20.6365 °2--0.5823 °2
S-0.0072 Å °-0.0226 Å °0.0067 Å °0.0898 Å °0.0548 Å °-0.1126 Å °0.024 Å °0.0267 Å °-0.0449 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 281
2X-RAY DIFFRACTION1allB24 - 281
3X-RAY DIFFRACTION1allS1 - 124

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