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- PDB-8buw: Crystal structure of Trichoplax Scribble PDZ1 domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 8buw
TitleCrystal structure of Trichoplax Scribble PDZ1 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 / Trichopla
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / adherens junction / cell-cell adhesion / basolateral plasma membrane / postsynaptic membrane / postsynaptic density / cytoplasm
Similarity search - Function
: / 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. ...: / 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
Leucine-rich repeat-containing protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
CitationJournal: To Be Published
Title: Crystal structure of Trichoplax Scribble PDZ1 domain in complex with Trichoplax Vangl peptide
Authors: Maddumage, J.C. / Kvansakul, M. / Humbert, P.O.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 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
D: Vang-like protein 1
C: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,7124
Polymers21,7124
Non-polymers00
Water00
1
A: Leucine-rich repeat-containing protein 1
D: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,8562
Polymers10,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area5380 Å2
MethodPISA
2
B: Leucine-rich repeat-containing protein 1
C: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,8562
Polymers10,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-4 kcal/mol
Surface area5270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.547, 30.298, 89.460
Angle α, β, γ (deg.)90.000, 90.920, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -1 through 10 or resid 12 through 79 or resid 82 through 90))
d_2ens_1(chain "B" and (resid -1 through 28 or (resid 29...
d_1ens_2chain "C"
d_2ens_2(chain "D" and (resid 66 through 71 or (resid 72...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYASPASPAA-1 - 104 - 15
d_12ens_1GLYGLYASNASNAA12 - 7917 - 84
d_13ens_1SERSERARGARGAA82 - 9087 - 95
d_21ens_1GLYGLYASNASNBB-1 - 794 - 84
d_22ens_1SERSERARGARGBB82 - 9087 - 95
d_11ens_2ASNASNVALVALDC66 - 731 - 8
d_21ens_2ASNASNVALVALCD193 - 2001 - 8

NCS ensembles :
ID
ens_1
ens_2

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Components

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


Mass: 9999.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / 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.: 2 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata)

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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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30% PEG 4000, 30% (v/v) ethylene glycol

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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 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.8→30.3 Å / Num. obs: 4011 / % possible obs: 96.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.59 Å2 / CC1/2: 0.954 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 587 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 2.85→29.82 Å / SU ML: 0.2848 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 200 5.27 %
Rwork0.2273 3597 -
obs0.2292 3797 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.64 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 0 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321467
X-RAY DIFFRACTIONf_angle_d0.61421967
X-RAY DIFFRACTIONf_chiral_restr0.0506232
X-RAY DIFFRACTIONf_plane_restr0.0032254
X-RAY DIFFRACTIONf_dihedral_angle_d13.6012537
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.03931156248
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.512996800343
LS refinement shellResolution: 2.85→29.82 Å
RfactorNum. reflection% reflection
Rfree0.2626 200 -
Rwork0.2273 3597 -
obs--94.85 %
Refinement TLS params.Method: refined / Origin x: -1.91077527322 Å / Origin y: -0.582042905752 Å / Origin z: -22.7954671098 Å
111213212223313233
T0.163772686233 Å20.0224620182733 Å2-0.0481417566589 Å2-0.0989517110912 Å20.00536403672506 Å2--0.0922918269124 Å2
L0.293518567241 °2-0.0935741976593 °20.0860567176268 °2-0.116459106194 °20.174711236381 °2--0.562279417082 °2
S0.0472418177264 Å °0.0486352055028 Å °0.053534288214 Å °-0.0438978665054 Å °0.0158710677829 Å °-0.0448799125361 Å °-0.0679340617934 Å °0.0172036714555 Å °0.118859824986 Å °
Refinement TLS groupSelection details: all

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