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- PDB-5oak: Structure of the dmPar3 PDZ1 domain in complex with the dmPar6 PBM -

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Basic information

Entry
Database: PDB / ID: 5oak
TitleStructure of the dmPar3 PDZ1 domain in complex with the dmPar6 PBM
ComponentsBazooka, isoform C,LD29223p
KeywordsPROTEIN BINDING / Cell polarity protein
Function / homology
Function and homology information


spot adherens junction / follicle cell of egg chamber-cell adhesion / border follicle cell delamination / germ-band extension / Malpighian tubule development / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex ...spot adherens junction / follicle cell of egg chamber-cell adhesion / border follicle cell delamination / germ-band extension / Malpighian tubule development / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity / RHOU GTPase cycle / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / photoreceptor cell morphogenesis / Asymmetric localization of PCP proteins / oocyte anterior/posterior axis specification / establishment or maintenance of polarity of embryonic epithelium / oocyte microtubule cytoskeleton organization / muscle cell postsynaptic specialization / germarium-derived oocyte fate determination / asymmetric protein localization involved in cell fate determination / border follicle cell migration / negative regulation of filopodium assembly / establishment of apical/basal cell polarity / establishment of centrosome localization / asymmetric neuroblast division / zonula adherens / morphogenesis of a polarized epithelium / apical cortex / phosphatidic acid binding / apical protein localization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / centrosome cycle / positive regulation of filopodium assembly / apical junction complex / establishment of cell polarity / protein kinase inhibitor activity / bicellular tight junction / positive regulation of lamellipodium assembly / synapse assembly / phosphatidylinositol binding / adherens junction / protein localization / terminal bouton / microtubule cytoskeleton organization / cell cortex / cell adhesion / cell cycle / apical plasma membrane / plasma membrane
Similarity search - Function
Partitioning defective protein 6, PB1 domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Partitioning defective protein 6, PB1 domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
LD29223p / Bazooka, isoform C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBruekner, S.R. / Wiesner, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max-Planck Gesellschaft Germany
IMPRS "From molecules to Organisms" Germany
CitationJournal: Sci Signal / Year: 2018
Title: Structural basis for the interaction between the cell polarity proteins Par3 and Par6.
Authors: Renschler, F.A. / Bruekner, S.R. / Salomon, P.L. / Mukherjee, A. / Kullmann, L. / Schutz-Stoffregen, M.C. / Henzler, C. / Pawson, T. / Krahn, M.P. / Wiesner, S.
History
DepositionJun 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bazooka, isoform C,LD29223p
B: Bazooka, isoform C,LD29223p
C: Bazooka, isoform C,LD29223p
D: Bazooka, isoform C,LD29223p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1035
Polymers49,0114
Non-polymers921
Water2,594144
1
A: Bazooka, isoform C,LD29223p
B: Bazooka, isoform C,LD29223p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5983
Polymers24,5062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area5910 Å2
MethodPISA
2
C: Bazooka, isoform C,LD29223p
D: Bazooka, isoform C,LD29223p


Theoretical massNumber of molelcules
Total (without water)24,5062
Polymers24,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-4 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.880, 60.880, 65.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Bazooka, isoform C,LD29223p / PAR-6 / Par-6 / isoform A / isoform B


Mass: 12252.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: dmPar3 PDZ1 domain with N-terminal cloning artifact (GAMG) fused to a C-terminal Gly-Ser-linker followed by the dmPar6 PBM (VKDGVLHL)
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: baz, CG5055, Dmel_CG5055, par-6, CG5884, Dmel_CG5884 / Plasmid: pET M41 / Production host: Escherichia coli (E. coli) / References: UniProt: X2JFU8, UniProt: O97111
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris pH 6.5, 2 M Ammoniumsulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.959 Å / Num. obs: 43343 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.241 % / Biso Wilson estimate: 23.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.045 / Χ2: 0.97 / Net I/σ(I): 26.63 / Num. measured all: 443891 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.549.2910.8482.5532180.7480.89898.9
1.54-1.5810.1010.6543.5931220.8870.689100
1.58-1.6210.0820.5084.6430160.920.536100
1.62-1.679.8840.386.1529660.9570.401100
1.67-1.739.7880.278.4128560.9760.285100
1.73-1.7910.6270.19711.5127970.9890.207100
1.79-1.8610.5240.14115.626550.9940.148100
1.86-1.9310.390.10420.4225800.9960.11100
1.93-2.029.830.07825.1624660.9980.083100
2.02-2.1210.3970.06132.1723410.9990.064100
2.12-2.2310.7810.05138.8622450.9990.054100
2.23-2.3710.6710.04841.1820980.9990.05100
2.37-2.5310.2810.04344.720090.9990.045100
2.53-2.7410.2320.03849.6618370.9990.04100
2.74-310.9980.03657.3217310.9990.037100
3-3.3510.7390.03362.2415300.9990.035100
3.35-3.879.8330.03264.2213640.9990.03499.9
3.87-4.7410.9320.03271.5311440.9990.034100
4.74-6.710.5320.03470.328880.9990.03699.9
6.7-40.95910.3250.03870.654800.9990.0499.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 1.5→40.959 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.46
RfactorNum. reflection% reflection
Rfree0.1691 2168 5 %
Rwork0.1403 --
obs0.1418 43341 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.16 Å2 / Biso mean: 32.18 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 1.5→40.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 6 144 1666
Biso mean--53.01 44.85 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151686
X-RAY DIFFRACTIONf_angle_d1.6362300
X-RAY DIFFRACTIONf_chiral_restr0.082269
X-RAY DIFFRACTIONf_plane_restr0.007308
X-RAY DIFFRACTIONf_dihedral_angle_d13.605701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.498-1.53290.26521460.19552756290299
1.5329-1.57120.21181420.155827102852100
1.5712-1.61370.17681460.132427722918100
1.6137-1.66120.19421430.12327142857100
1.6612-1.71480.15741450.111927582903100
1.7148-1.77610.16341450.109227462891100
1.7761-1.84720.15031460.104627852931100
1.8472-1.93130.1641420.105726862828100
1.9313-2.03310.16721460.107427822928100
2.0331-2.16050.15571430.116527142857100
2.1605-2.32730.17451450.128227692914100
2.3273-2.56140.17831450.145527362881100
2.5614-2.9320.18851450.154227722917100
2.932-3.69360.17341440.151127282872100
3.6936-40.97470.15291450.154427452890100

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