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- PDB-8c1t: Crystal structure of Trichoplax Dlg PDZ1 domain in complex with T... -

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Basic information

Entry
Database: PDB / ID: 8c1t
TitleCrystal structure of Trichoplax Dlg PDZ1 domain in complex with Trichoplax Vangl peptide
Components
  • Disks large-like protein 1
  • Vang-like protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Dlg / Vangl / 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
MALONIC ACID / Vang-like protein 1 / Disks large-like protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 Dlg PDZ1 domain in complex with Trichoplax Vangl peptide
Authors: Maddumage, J.C. / Kvansakul, M.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Disks large-like protein 1
A: Disks large-like protein 1
B: Disks large-like protein 1
C: Disks large-like protein 1
E: Vang-like protein 1
F: Vang-like protein 1
G: Vang-like protein 1
H: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,45211
Polymers43,1408
Non-polymers3123
Water2,432135
1
D: Disks large-like protein 1
E: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,7852
Polymers10,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Disks large-like protein 1
F: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,7852
Polymers10,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Disks large-like protein 1
G: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9934
Polymers10,7852
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Disks large-like protein 1
H: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8893
Polymers10,7852
Non-polymers1041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.696, 47.953, 50.830
Angle α, β, γ (deg.)85.250, 72.080, 69.170
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or (resid 11...
d_2ens_1(chain "B" and (resid 1 through 10 or (resid 11...
d_3ens_1(chain "C" and (resid 1 through 23 or (resid 24...
d_4ens_1(chain "D" and (resid 1 through 10 or (resid 11...
d_1ens_2(chain "E" and (resid 116 through 122 or (resid 123...
d_2ens_2chain "F"
d_3ens_2(chain "G" and (resid 48 through 54 or (resid 55...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERB2 - 79
d_12ens_1GLYARGB81 - 90
d_21ens_1GLNSERC2 - 79
d_22ens_1GLYARGC81 - 90
d_31ens_1GLNSERF1 - 78
d_32ens_1GLYARGF80 - 89
d_41ens_1GLNARGA2 - 89
d_11ens_2ASNVALH1 - 8
d_21ens_2ASNVALI1 - 8
d_31ens_2ASNVALJ1 - 8

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.92674991047, 0.214976796485, 0.308090214737), (-0.0347581556908, 0.767506107294, -0.640098621994), (-0.374067472599, -0.603919988276, -0.703814019258)11.9104237503, -9.76434247486, 14.9838816602
2given(-0.927876811756, 0.229921027989, 0.293565909284), (0.0102413100797, -0.771268345651, 0.636427729255), (0.372746210944, 0.593533031841, 0.713287321029)29.3612730665, -8.07453369715, 4.30315987803
3given(0.999867876545, 0.0161926596162, 0.00142380745098), (0.0161505445344, -0.999536485976, 0.025806454871), (0.00184102263588, -0.0257800499674, -0.999665944033)17.5108845343, -18.0106583031, 19.0527293237
4given(0.999829474351, 0.00034320317063, -0.0184635974629), (0.000675087911356, -0.999838265231, 0.0179718567562), (-0.018454443259, -0.0179812566451, -0.999667998854)-16.6554112967, -18.3765611596, 20.2261015266
5given(-0.730186026261, -0.330123065579, -0.598203250264), (0.158646416697, -0.933518099265, 0.321520252573), (-0.664574812585, 0.139866793478, 0.734014712768)33.089278161, -30.0029115125, 27.459253049

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Components

#1: Protein
Disks large-like protein 1


Mass: 9928.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_000924 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A369SI82
#2: Protein/peptide
Vang-like protein 1


Mass: 856.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata) / References: UniProt: A0A369S4B9
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.81 Å3/Da / Density % sol: 32.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.2 M sodium malonate dibasic monohydrate, pH 6.1 , 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: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.2→44.8 Å / Num. obs: 14440 / % possible obs: 97.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.57 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1247 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RL7

3rl7


Resolution: 2.2→33.36 Å / SU ML: 0.3283 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.0308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2643 759 5.26 %
Rwork0.2112 13672 -
obs0.2141 14431 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 21 135 3037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012933
X-RAY DIFFRACTIONf_angle_d0.94783968
X-RAY DIFFRACTIONf_chiral_restr0.0588460
X-RAY DIFFRACTIONf_plane_restr0.0061532
X-RAY DIFFRACTIONf_dihedral_angle_d12.50081068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS1.39315263274
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS1.44752972197
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS0.756310401046
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.617693174915
ens_2d_3HX-RAY DIFFRACTIONTorsion NCS3.41417078542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.34271410.262705X-RAY DIFFRACTION96.7
2.37-2.610.35651290.25942752X-RAY DIFFRACTION97.5
2.61-2.990.30811840.23452703X-RAY DIFFRACTION97.24
2.99-3.760.2381440.1912760X-RAY DIFFRACTION98.31
3.76-33.360.20931610.1812752X-RAY DIFFRACTION98.55
Refinement TLS params.Method: refined / Origin x: 12.594167925 Å / Origin y: -9.18082368524 Å / Origin z: 9.81651069256 Å
111213212223313233
T0.168766655285 Å2-0.00440242416384 Å20.0396464690876 Å2-0.189089627167 Å20.0425201608725 Å2--0.401570409623 Å2
L0.106751693808 °20.111136042419 °2-0.0679082083054 °2-0.21996308948 °2-0.125835261077 °2--0.333039538063 °2
S-0.0160435728072 Å °-0.000614530001234 Å °-0.0230453323008 Å °-6.84405416721E-5 Å °-0.020817846192 Å °-0.017590690569 Å °-0.00578281760018 Å °-0.00308785120555 Å °0.0355898969563 Å °
Refinement TLS groupSelection details: all

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