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- PDB-1ijx: CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLE... -

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Basic information

Entry
Database: PDB / ID: 1ijx
TitleCRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLED-RELATED PROTEIN 3 (SFRP-3;FZB)
ComponentsSECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
KeywordsSIGNALING PROTEIN / WNT RECEPTOR / FRIZZLED PROTEIN STRUCTURE / CYSTEINE-RICH
Function / homology
Function and homology information


negative regulation of hepatocyte differentiation / negative regulation of cell development / convergent extension involved in organogenesis / negative regulation of cartilage development / somite development / cochlea morphogenesis / Wnt-protein binding / hepatocyte differentiation / neural crest cell differentiation / inner ear morphogenesis ...negative regulation of hepatocyte differentiation / negative regulation of cell development / convergent extension involved in organogenesis / negative regulation of cartilage development / somite development / cochlea morphogenesis / Wnt-protein binding / hepatocyte differentiation / neural crest cell differentiation / inner ear morphogenesis / epithelial cell development / negative regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / Wnt signaling pathway / positive regulation of apoptotic process / negative regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Secreted frizzled-related protein 3, NTR domain / SFRP3, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Secreted frizzled-related protein 3, NTR domain / SFRP3, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Secreted frizzled-related protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J.
CitationJournal: Nature / Year: 2001
Title: Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains.
Authors: Dann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J.
History
DepositionApr 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 28, 2014Group: Structure summary
Revision 1.4May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
B: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
C: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
D: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
E: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
F: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2937
Polymers85,1976
Non-polymers961
Water8,989499
1
A: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
C: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4953
Polymers28,3992
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-36 kcal/mol
Surface area13120 Å2
MethodPISA
2
B: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
E: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)28,3992
Polymers28,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-21 kcal/mol
Surface area12380 Å2
MethodPISA
3
D: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3

F: SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)28,3992
Polymers28,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2430 Å2
ΔGint-23 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.050, 48.690, 83.310
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3


Mass: 14199.509 Da / Num. of mol.: 6 / Fragment: CYSTEINE-RICH DOMAIN / Mutation: N17E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SFRP-3 / Plasmid: PSGHV0 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P97401
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 3350, PEG 400, Sodium Hepes, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.1 MHEPES1reservoir
312 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9203 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9203 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 61210 / Num. obs: 61070 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6167 / % possible all: 98.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
Omodel building
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 6189 -RANDOM
Rwork0.22 ---
all-61210 --
obs-61070 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5799 0 5 499 6303
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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