8BNB | pdb_00008bnb

Crystal structure of Trichoplax Scribble PDZ2 domain

• PDB DOI: https://doi.org/10.2210/pdb8BNB/pdb

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


• Deposited: 2022-11-14 Released: 2023-11-29 
• Deposition Author(s): Maddumage, J.C., Kvansakul, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Trichoplax Scribble PDZ2 domain

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 20.17 kDa 
• Atom Count: 1,415 
• Modeled Residue Count: 189 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing protein 1	A, B	95	Trichoplax sp. H2	Mutation(s): 0  Gene Names: TrispH2_005790
UniProt
Find proteins for A0ACD6BAH4 (Trichoplax sp. H2) Explore A0ACD6BAH4  Go to UniProtKB:  A0ACD6BAH4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.781	α = 93.63
b = 32.946	β = 95.65
c = 42.71	γ = 113.74

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: 2023-11-29 
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
Australian Research Council (ARC)	Australia	FT130101349

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary