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- PDB-8bpm: Crystal structure of Trichoplax Dlg PDZ3 domain -

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Basic information

Entry
Database: PDB / ID: 8bpm
TitleCrystal structure of Trichoplax Dlg PDZ3 domain
ComponentsDisks large-like protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Dlg
Function / homology
Function and homology information


receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / cell-cell adhesion / cell junction / basolateral plasma membrane / protein kinase binding
Similarity search - Function
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 ...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
Disks large-like protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 PDZ3 domain
Authors: Maddumage, J.C. / Kvansakul, M. / Humbert, P.O.
History
DepositionNov 17, 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: Disks large-like protein 1
B: Disks large-like protein 1
C: Disks large-like protein 1
D: Disks large-like protein 1


Theoretical massNumber of molelcules
Total (without water)39,8364
Polymers39,8364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.375, 35.434, 72.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 12 through 84 or (resid 85...
d_2ens_1(chain "B" and resid 12 through 102)
d_3ens_1(chain "C" and (resid 12 through 99 or (resid 100...
d_4ens_1(chain "D" and (resid 12 through 99 or (resid 100...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 12 - 102 / Label seq-ID: 1 - 91

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.999994747545, -0.000970053042481, 0.00309255218828), (0.000970495329763, -0.999999519055, 0.000141519468049), (0.00309241341954, 0.00014452003218, 0.999995208035)16.2185034696, -35.2608292072, -36.5148920579
2given(-0.999998132603, 0.000200673717584, 0.00192211338659), (0.00020474943004, 0.999997730838, 0.00212047088255), (-0.00192168350223, 0.00212086047441, -0.999995904533)32.4053901615, 0.0178172806333, -73.2853843361
3given(0.999983618473, 0.00180497855184, -0.00543183563373), (0.00179755570538, -0.999997444413, -0.00137111666965), (-0.00543429658838, 0.00136133018153, -0.999984307477)16.1740552599, -35.312025621, -36.7369749407

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Components

#1: Protein
Disks large-like protein 1


Mass: 9959.068 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) / Strain (production host): Codon+ / References: UniProt: A0A369SI82

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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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG 1500

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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: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.8→25.42 Å / Num. obs: 7852 / % possible obs: 98.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.53 Å2 / CC1/2: 0.975 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 1188 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I4W

3i4w


Resolution: 2.8→25.42 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.3515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 389 4.96 %
Rwork0.2078 7453 -
obs0.2098 7842 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 0 0 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522787
X-RAY DIFFRACTIONf_angle_d0.73273766
X-RAY DIFFRACTIONf_chiral_restr0.0504412
X-RAY DIFFRACTIONf_plane_restr0.0066515
X-RAY DIFFRACTIONf_dihedral_angle_d14.26781036
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.311476139895
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.31764201943
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.805739598469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20.33021620.26352462X-RAY DIFFRACTION97.55
3.2-4.030.29821140.20912496X-RAY DIFFRACTION98.6
4.04-25.420.15661130.17482495X-RAY DIFFRACTION98.49

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