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- PDB-5m0w: N-terminal domain of mouse Shisa 3 -

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Basic information

Entry
Database: PDB / ID: 5m0w
TitleN-terminal domain of mouse Shisa 3
ComponentsProtein shisa-3 homolog
KeywordsSIGNALING PROTEIN / Single-pass transmembrane protein / tumor suppressor gene / Wnt-signaling pathway / disulfide
Function / homologyShisa family / : / Shisa, N-terminal domain / negative regulation of canonical Wnt signaling pathway / endoplasmic reticulum membrane / DI(HYDROXYETHYL)ETHER / Protein shisa-3 homolog
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLohkamp, B. / Ojala, J.R.M.
Funding support Sweden, Denmark, 4items
OrganizationGrant numberCountry
VR2007-5648 Sweden
Knut and Alice Wallenberg Foundation Sweden
VR Sweden
Novo Nordisk Foundation Denmark
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Ab initio solution of macromolecular crystal structures without direct methods.
Authors: McCoy, A.J. / Oeffner, R.D. / Wrobel, A.G. / Ojala, J.R. / Tryggvason, K. / Lohkamp, B. / Read, R.J.
#1: Journal: To Be Published
Title: Ab initio solution of macromolecular crystal structures without direct methods
Authors: McCoy, A.J. / Oeffner, R.D. / Wrobel, A. / Ojala, J.R.M. / Tryggvason, K. / Lohkamp, B. / Read, R.J.
History
DepositionOct 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 2.0Mar 11, 2020Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_special_symmetry / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein shisa-3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,99711
Polymers9,0411
Non-polymers95610
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-21 kcal/mol
Surface area4550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.765, 59.765, 48.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein shisa-3 homolog


Mass: 9040.780 Da / Num. of mol.: 1 / Fragment: UNP residues 22-95
Source method: isolated from a genetically manipulated source
Details: N-terminal domain with Strep tag / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shisa3 / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): H5 / References: UniProt: Q3UPR0

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Non-polymers , 6 types, 118 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.0 M (NH4)2SO4, 100 mM MES pH 6.5, 4% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.39→29.88 Å / Num. obs: 18352 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.5
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.879 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single sulphur

Resolution: 1.39→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.276 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13668 935 5.1 %RANDOM
Rwork0.11535 ---
obs0.11644 17366 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0 Å2
2--0.14 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.39→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 59 108 641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019591
X-RAY DIFFRACTIONr_bond_other_d0.0040.02487
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.984799
X-RAY DIFFRACTIONr_angle_other_deg1.1422.9911137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.467573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01824.86537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1271577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.191153
X-RAY DIFFRACTIONr_chiral_restr0.1120.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02136
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_it1.751.583267
X-RAY DIFFRACTIONr_mcbond_other1.591.555265
X-RAY DIFFRACTIONr_mcangle_it2.0612.361335
X-RAY DIFFRACTIONr_mcangle_other2.0582.377336
X-RAY DIFFRACTIONr_scbond_it2.912.147323
X-RAY DIFFRACTIONr_scbond_other2.8652.147323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.353.04458
X-RAY DIFFRACTIONr_long_range_B_refined4.18123.658672
X-RAY DIFFRACTIONr_long_range_B_other3.75822.297646
X-RAY DIFFRACTIONr_rigid_bond_restr7.99931075
X-RAY DIFFRACTIONr_sphericity_free29.17168
X-RAY DIFFRACTIONr_sphericity_bonded10.90311109
LS refinement shellResolution: 1.385→1.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 58 -
Rwork0.317 1159 -
obs--90.96 %

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