8BV7 | pdb_00008bv7

Crystal structure of the Trichoplax Scribble PDZ1 domain in complex with the Trichoplax phosphorylated Vangl peptide

• PDB DOI: https://doi.org/10.2210/pdb8BV7/pdb

• Classification: PROTEIN BINDING
• Organism(s): Trichoplax sp. H2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-12-02 Released: 2023-12-13 
• Deposition Author(s): Maddumage, J.C., Kvansakul, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Trichoplax Scribble PDZ1 domain in complex with Trichoplax the phosphorylated Vangl peptide

Maddumage, J.C., Kvansakul, M., Humbert, P.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 10.94 kDa 
• Atom Count: 812 
• Modeled Residue Count: 103 
• Deposited Residue Count: 104 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing protein 1	A	96	Trichoplax sp. H2	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vang-like protein 1	B	8	Trichoplax sp. H2	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.092	α = 90
b = 45.236	β = 90
c = 70.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Maddumage, J.C., Kvansakul, M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1103871

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary