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- PDB-8bp4: Crystal structure of Trichoplax Scribble PDZ2 domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 8bp4
TitleCrystal structure of Trichoplax Scribble PDZ2 domain in complex with Trichoplax Vangl peptide
Components
  • Leucine-rich repeat-containing protein 1
  • Vang-like protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Scribble / Vangl / Trichoplax
Function / homology
Function and homology information


receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / adherens junction / cell-cell adhesion / basolateral plasma membrane / protein kinase binding
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
AMMONIUM ION / Leucine-rich repeat-containing protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: To be published
Title: Crystal structure of Trichoplax Scribble PDZ2 domain in complex with Trichoplax Vangl peptide
Authors: Maddumage, J.C. / Humbert, P.O. / Kvansakul, M.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 1
B: Leucine-rich repeat-containing protein 1
C: Leucine-rich repeat-containing protein 1
D: Vang-like protein 1
E: Vang-like protein 1
F: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,85414
Polymers32,2416
Non-polymers6128
Water4,558253
1
A: Leucine-rich repeat-containing protein 1
D: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0717
Polymers10,7472
Non-polymers3245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-36 kcal/mol
Surface area5940 Å2
MethodPISA
2
B: Leucine-rich repeat-containing protein 1
hetero molecules

E: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,9394
Polymers10,7472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area390 Å2
ΔGint-14 kcal/mol
Surface area5830 Å2
MethodPISA
3
F: Vang-like protein 1
hetero molecules

C: Leucine-rich repeat-containing protein 1


Theoretical massNumber of molelcules
Total (without water)10,8433
Polymers10,7472
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area550 Å2
ΔGint-21 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.303, 43.387, 71.316
Angle α, β, γ (deg.)90.000, 91.080, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Leucine-rich repeat-containing protein 1


Mass: 9890.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_005790 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): codon + / References: UniProt: A0A369S7Y8
#2: Protein/peptide Vang-like protein 1


Mass: 856.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata)
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H4N
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.96 % / Description: Cubes
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.15→43.39 Å / Num. obs: 91308 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.5
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 1.328 / Num. unique obs: 4253 / CC1/2: 0.337

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JO7

7jo7


Resolution: 1.15→42.3 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2108 4463 4.9 %
Rwork0.1783 86693 -
obs0.1799 91156 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.85 Å2
Refinement stepCycle: LAST / Resolution: 1.15→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 32 253 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01782139
X-RAY DIFFRACTIONf_angle_d1.4592882
X-RAY DIFFRACTIONf_chiral_restr0.1038347
X-RAY DIFFRACTIONf_plane_restr0.0108361
X-RAY DIFFRACTIONf_dihedral_angle_d13.6343772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.42651420.38952581X-RAY DIFFRACTION89.81
1.16-1.180.35691470.36052843X-RAY DIFFRACTION96.36
1.18-1.190.39321700.33612773X-RAY DIFFRACTION97.94
1.19-1.210.32651560.31382883X-RAY DIFFRACTION98.83
1.21-1.220.31871530.29712810X-RAY DIFFRACTION99.4
1.22-1.240.33271500.28122903X-RAY DIFFRACTION99.64
1.24-1.260.30911520.27812863X-RAY DIFFRACTION99.6
1.26-1.280.29121840.26432885X-RAY DIFFRACTION99.93
1.28-1.30.32021550.25352839X-RAY DIFFRACTION99.87
1.3-1.320.29861410.2432948X-RAY DIFFRACTION99.94
1.32-1.340.27021220.23922892X-RAY DIFFRACTION99.97
1.34-1.360.30961070.23372958X-RAY DIFFRACTION99.93
1.36-1.390.27691440.212892X-RAY DIFFRACTION99.9
1.39-1.420.26771530.20722939X-RAY DIFFRACTION100
1.42-1.450.26581510.19412869X-RAY DIFFRACTION99.93
1.45-1.480.2481640.17872870X-RAY DIFFRACTION99.77
1.48-1.520.21611530.16672933X-RAY DIFFRACTION99.87
1.52-1.560.23141560.15512868X-RAY DIFFRACTION99.77
1.56-1.610.19831470.15162926X-RAY DIFFRACTION99.93
1.61-1.660.20651580.15112889X-RAY DIFFRACTION99.9
1.66-1.720.21791320.15982898X-RAY DIFFRACTION99.97
1.72-1.790.22091260.1642977X-RAY DIFFRACTION99.94
1.79-1.870.2281560.15722874X-RAY DIFFRACTION99.77
1.87-1.970.24131210.15662952X-RAY DIFFRACTION99.87
1.97-2.090.19251400.15132929X-RAY DIFFRACTION99.87
2.09-2.250.18691780.15252908X-RAY DIFFRACTION100
2.25-2.480.19171560.16572906X-RAY DIFFRACTION99.87
2.48-2.840.22241260.17332975X-RAY DIFFRACTION99.81
2.84-3.570.21321610.17562951X-RAY DIFFRACTION99.81
3.57-42.30.16891620.18052959X-RAY DIFFRACTION98.27

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