7PBF

Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-mannuronic acid

PDB DOI: https://doi.org/10.2210/pdb7PBF/pdb

Classification: LYASE
Organism(s): Paradendryphiella salina
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2021-08-02 Released: 2022-08-10
Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.195
R-Value Work: 0.171
R-Value Observed: 0.172

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-mannuronic acid

Fredslund, F., Welner, D.H., Wilkens, C.

To be published.

Macromolecule Content

Total Structure Weight: 25.84 kDa
Atom Count: 1,929
Modelled Residue Count: 226
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase (PL7)	A	231	Paradendryphiella salina	Mutation(s): 0 Gene Names: PsAlg7A
UniProt
Find proteins for A0A485PVH1 (Paradendryphiella salina) Explore A0A485PVH1 Go to UniProtKB: A0A485PVH1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A485PVH1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	B	2	N/A	N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G11270VO GlyCosmos: G11270VO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.195
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35	α = 90
b = 80.64	β = 90
c = 81.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union (EU)	European Union	9082-00021B

Revision History (Full details and data files)

Version 1.0: 2022-08-10
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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.