7O6H

Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with tri-mannuronic acid

PDB DOI: https://doi.org/10.2210/pdb7O6H/pdb

Classification: LYASE
Organism(s): Paradendryphiella salina
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2021-04-11 Released: 2022-04-20
Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.204
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with tri-mannuronic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 26.19 kDa
Atom Count: 1,939
Modelled Residue Count: 226
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase (PL7)	A	231	Paradendryphiella salina	Mutation(s): 1 Gene Names: PsAlg7A EC: 4.2.2.3
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)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G85027VZ GlyCosmos: G85027VZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAV (Subject of Investigation/LOI) Query on MAV Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	alpha-D-mannopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-BYHBOUFCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.204
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.98	α = 90
b = 81.22	β = 90
c = 80.8	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.