8BOJ | pdb_00008boj

Crystal structure of Trichoplax Scribble PDZ1 domain

PDB DOI: https://doi.org/10.2210/pdb8BOJ/pdb

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

Deposited: 2022-11-15 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: 1.50 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Trichoplax Pals1 PDZ1 with Trichoplax Crumbs peptide

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

To be published.

Macromolecule Content

Total Structure Weight: 10 kDa
Atom Count: 822
Modeled Residue Count: 96
Deposited Residue Count: 96
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.067	α = 90
b = 49.016	β = 90
c = 68.873	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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

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.