7NPP

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

PDB DOI: https://doi.org/10.2210/pdb7NPP/pdb

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

Deposited: 2021-02-28 Released: 2022-03-23
Deposition Author(s): Fredslund, F., Welner, D.W., Wilkens, C.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.187
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 26.56 kDa
Atom Count: 2,114
Modelled Residue Count: 227
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): 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-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid	B	5		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G61688UV GlyCosmos: G61688UV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.187
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.83	α = 90
b = 80.74	β = 90
c = 81.31	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.