8TNF

Crystal structure of sulfohexulose-1-phosphate aldolase from Paracoccus onubensis strain Merri

PDB DOI: https://doi.org/10.2210/pdb8TNF/pdb

Classification: LYASE
Organism(s): Paracoccus onubensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-01 Released: 2024-08-07
Deposition Author(s): Lee, M.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282
R-Value Work: 0.237
R-Value Observed: 0.239

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

A patchwork pathway for catabolism degradation of the sulfosugar sulfofucose

Li, J., Lee, M., Yang, S., Lewis, J.M., Herisse, M., Pidot, S.J., Scott, N.E., Williams, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 321.21 kDa
Atom Count: 21,084
Modelled Residue Count: 2,663
Deposited Residue Count: 2,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF2090 domain-containing protein	A, B, C, D, E A, B, C, D, E, F, G, H	362	Paracoccus onubensis	Mutation(s): 0 Gene Names: D3P04_00185
UniProt
Find proteins for A0A418T8G4 (Paracoccus onubensis) Explore A0A418T8G4 Go to UniProtKB: A0A418T8G4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A418T8G4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282
R-Value Work: 0.237
R-Value Observed: 0.239
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.663	α = 96.05
b = 82.485	β = 90
c = 144.77	γ = 97.42

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP210100233, DP210100233

Revision History (Full details and data files)

Version 1.0: 2024-08-07
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 R01GM133198.