8BP5 | pdb_00008bp5

Crystal structure of Trichoplax Dlg PDZ1 domain

PDB DOI: https://doi.org/10.2210/pdb8BP5/pdb

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

Deposited: 2022-11-16 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Trichoplax Dlg PDZ1 domain

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

To be published.

Macromolecule Content

Total Structure Weight: 19.55 kDa
Atom Count: 1,446
Modeled Residue Count: 181
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large-like protein 1	A, B	92	Trichoplax sp. H2	Mutation(s): 0 Gene Names: TrispH2_000924
UniProt
Find proteins for A0ACD6BAH5 (Trichoplax sp. H2) Explore A0ACD6BAH5 Go to UniProtKB: A0ACD6BAH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.242 (Depositor), 0.243 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.962	α = 90
b = 52.632	β = 92.93
c = 43.005	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Maddumage, J.C.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1103871
Australian Research Council (ARC)	Australia	FT130101349

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.