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- PDB-8bq8: Crystal structure of Trichoplax Dlg PDZ2 domain in complex with T... -

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Basic information

Entry
Database: PDB / ID: 8bq8
TitleCrystal structure of Trichoplax Dlg PDZ2 domain in complex with Trichoplax Vangl peptide
Components
  • Disks large-like protein 1
  • Vang-like protein 1
KeywordsPROTEIN BINDING / Dlg / PDZ domain / Cell polarity / Trichoplax
Function / homology
Function and homology information


embryo development / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / chemical synaptic transmission / basolateral plasma membrane / neuron projection / plasma membrane
Similarity search - Function
Vang-like protein / Strabismus protein / L27-1 / L27_1 / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit ...Vang-like protein / Strabismus protein / L27-1 / L27_1 / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Vang-like protein 1 / Disks large-like protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMadduamge, 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 Dlg PDZ2 domain in complex with Trichoplax Vangl peptide
Authors: Madduamge, J.C. / Kvansakul, M. / Humbert, P.O.
History
DepositionNov 20, 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: Disks large-like protein 1
B: Disks large-like protein 1
C: Disks large-like protein 1
D: Vang-like protein 1
F: Vang-like protein 1
E: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)32,2726
Polymers32,2726
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.673, 101.980, 106.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 316 through 325 or (resid 326...
d_2ens_1(chain "B" and (resid 316 through 360 or (resid 361...
d_3ens_1(chain "C" and (resid 316 through 324 or (resid 325...
d_1ens_2chain "D"
d_2ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROA1 - 89
d_21ens_1SERPROB2 - 90
d_31ens_1SERASPC4 - 14
d_32ens_1GLYPROC16 - 93
d_11ens_2PROVALD1 - 5
d_21ens_2PROVALE1 - 5

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.671590763585, 0.18141648297, -0.718368920524), (0.149530878418, -0.916423032504, -0.371226806543), (-0.72567648623, -0.356730830183, 0.588333878108)-0.607554830378, -48.9917741389, -11.5001009469
2given(-0.445316281924, -0.647315153297, -0.618608520282), (0.527979774779, 0.368151749367, -0.765311470489), (0.723139520755, -0.667418445767, 0.177825340638)-27.0894198399, -19.7356594867, -30.865348117
3given(-0.520799615416, -0.624968609361, -0.581534176034), (0.528341794665, 0.299100667571, -0.79460288111), (0.670539117869, -0.721077685115, 0.174425524037)-26.6905411008, -20.4928613577, -31.1835695691

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Components

#1: Protein Disks large-like protein 1


Mass: 9900.308 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_000924 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A369SI82
#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) / References: UniProt: A0A369S4B9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 6.5, 20% glucose

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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: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.7→48.54 Å / Num. obs: 9739 / % possible obs: 98.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.982 / Net I/σ(I): 7.3
Reflection shellResolution: 2.7→2.77 Å / Num. unique obs: 716 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G69

4g69


Resolution: 2.7→32.34 Å / SU ML: 0.3209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2715 517 5.32 %
Rwork0.2223 9195 -
obs0.225 9712 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.58 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 0 53 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322135
X-RAY DIFFRACTIONf_angle_d0.62542887
X-RAY DIFFRACTIONf_chiral_restr0.0549365
X-RAY DIFFRACTIONf_plane_restr0.0029370
X-RAY DIFFRACTIONf_dihedral_angle_d10.5595760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.712162969521
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.881724693583
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.715162203334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.37631080.30262274X-RAY DIFFRACTION98.02
2.97-3.40.32511250.26562309X-RAY DIFFRACTION99.02
3.4-4.280.25511370.19982284X-RAY DIFFRACTION98.14
4.28-32.340.22781470.18212328X-RAY DIFFRACTION95.82
Refinement TLS params.Method: refined / Origin x: -5.52506690602 Å / Origin y: -24.0628698113 Å / Origin z: -12.1668841938 Å
111213212223313233
T0.150257535428 Å20.0149981999793 Å20.0402064192766 Å2-0.154238540329 Å20.0469019342433 Å2--0.145749870035 Å2
L1.8577085229 °20.203274593673 °20.0140425424263 °2-1.2332093558 °20.723300638657 °2--1.87773677969 °2
S-0.126661764197 Å °-0.0865232990803 Å °-0.122245931601 Å °0.0674132352288 Å °0.0372319443082 Å °0.0136478902207 Å °0.0725720020133 Å °-0.0172781912796 Å °0.043050685729 Å °
Refinement TLS groupSelection details: all

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