8BPM | pdb_00008bpm

Crystal structure of Trichoplax Dlg PDZ3 domain

• PDB DOI: https://doi.org/10.2210/pdb8BPM/pdb

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


• Deposited: 2022-11-17 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: 2.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Trichoplax Dlg PDZ3 domain

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.84 kDa 
• Atom Count: 2,743 
• Modeled Residue Count: 368 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large-like protein 1	A, B, C, D	93	Trichoplax sp. H2	Mutation(s): 0  Gene Names: TrispH2_000924

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.375	α = 90
b = 35.434	β = 90
c = 72.99	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: 2023-11-29 
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