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- PDB-5xgp: structure of Sizzled from Xenopus laevis at 2.08 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 5xgp
Titlestructure of Sizzled from Xenopus laevis at 2.08 angstroms resolution
ComponentsSecreted Xwnt8 inhibitor sizzled
KeywordsUNKNOWN FUNCTION / secreted protein
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: 2.077 Å
AuthorsLiu, H. / Li, Z. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81322047 China
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The crystal structure of full-length Sizzled from Xenopus laevis yields insights into Wnt-antagonistic function of secreted Frizzled-related proteins
Authors: Bu, Q. / Li, Z. / Zhang, J. / Xu, F. / Liu, J. / Liu, H.
History
DepositionApr 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.3Dec 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted Xwnt8 inhibitor sizzled
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,26912
Polymers29,7571
Non-polymers51111
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Indeed, as shown in size-exclusion chromatography, the elution volume of Sizzled on a Supedex 200 column was 16.2 ml, a volume corresponding to an eluted protein with an ...Evidence: gel filtration, Indeed, as shown in size-exclusion chromatography, the elution volume of Sizzled on a Supedex 200 column was 16.2 ml, a volume corresponding to an eluted protein with an apparent molecular weight of ~35 kD. As seen in the same figure, Sizzled migrated as a band on a SDS-PAGE gel, equivalent to a MW of ~ 33 kD. These results show that Sizzled exists as a monomer in the solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.131, 70.131, 132.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Secreted Xwnt8 inhibitor sizzled


Mass: 29757.486 Da / Num. of mol.: 1 / Fragment: UNP residues 24-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: szl / Cell line (production host): 293 GnTI / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O73821
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG8K, 0.1 M imidazole (pH 8.0) and 0.2 M lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 20594 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Χ2: 1.591 / Net I/av σ(I): 30.1 / Net I/σ(I): 30.1
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1014 / CC1/2: 0.824 / Rpim(I) all: 0.423 / Χ2: 1.325 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.077→19.855 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 989 4.81 %RANDOM
Rwork0.2135 ---
obs0.2143 20553 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.077→19.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 19 107 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022049
X-RAY DIFFRACTIONf_angle_d0.4572783
X-RAY DIFFRACTIONf_dihedral_angle_d12.1351262
X-RAY DIFFRACTIONf_chiral_restr0.038305
X-RAY DIFFRACTIONf_plane_restr0.003352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0768-2.18620.31941630.2772690X-RAY DIFFRACTION99
2.1862-2.3230.36941340.28232754X-RAY DIFFRACTION100
2.323-2.5020.28451350.24572778X-RAY DIFFRACTION100
2.502-2.75320.27021130.26172778X-RAY DIFFRACTION100
2.7532-3.15030.28781410.24182785X-RAY DIFFRACTION99
3.1503-3.96380.20741340.20412828X-RAY DIFFRACTION99
3.9638-19.85550.1921690.18192951X-RAY DIFFRACTION99

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