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- PDB-8boj: Crystal structure of Trichoplax Scribble PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 8boj
TitleCrystal structure of Trichoplax Scribble PDZ1 domain
ComponentsLeucine-rich repeat-containing protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / scribble / Trichoplax
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / 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. / PDZ domain ...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: 1.5 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 Pals1 PDZ1 with Trichoplax Crumbs peptide
Authors: Maddumage, J.C. / Humbert, P.O. / Kvansakul, M.
History
DepositionNov 15, 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

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 1


Theoretical massNumber of molelcules
Total (without water)9,9991
Polymers9,9991
Non-polymers00
Water2,234124
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)24.067, 49.016, 68.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 9999.283 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium citrate, pH 5.7

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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: Apr 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.5→49.02 Å / Num. obs: 13564 / % possible obs: 99.1 % / Redundancy: 13 % / Biso Wilson estimate: 11.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 657 / CC1/2: 0.906

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Processing

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

5vwc


Resolution: 1.5→39.93 Å / SU ML: 0.1592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 696 5.15 %
Rwork0.1814 12825 -
obs0.1829 13521 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.46 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 0 124 822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042705
X-RAY DIFFRACTIONf_angle_d0.7103945
X-RAY DIFFRACTIONf_chiral_restr0.0526110
X-RAY DIFFRACTIONf_plane_restr0.0067122
X-RAY DIFFRACTIONf_dihedral_angle_d10.8931260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.620.23321350.1992480X-RAY DIFFRACTION97.94
1.62-1.780.21131310.18092501X-RAY DIFFRACTION98.8
1.78-2.040.22391360.17752552X-RAY DIFFRACTION98.64
2.04-2.560.171300.18072581X-RAY DIFFRACTION99.45
2.57-39.930.21881640.18012711X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 10.4769354893 Å / Origin y: 0.277246687908 Å / Origin z: -14.0762643124 Å
111213212223313233
T0.0605976990269 Å2-0.00340526561955 Å20.00398070142189 Å2-0.076648179295 Å2-0.00124654680743 Å2--0.0756258837126 Å2
L1.63300718689 °2-0.272752851089 °20.0377117278965 °2-1.91450396403 °2-0.289822856614 °2--1.56835424356 °2
S0.0290655463966 Å °-0.0402531168968 Å °0.00157529337732 Å °0.112402570829 Å °-0.0240350056285 Å °0.0307638215924 Å °-0.00848451569512 Å °-0.0410509779031 Å °-0.0126983113805 Å °
Refinement TLS groupSelection details: all

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