8BXZ

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid

PDB DOI: https://doi.org/10.2210/pdb8BXZ/pdb

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

Deposited: 2022-12-11 Released: 2023-12-20
Deposition Author(s): Wilkens, C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.141
R-Value Work: 0.115
R-Value Observed: 0.116

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid

Wilkens, C.

To be published.

Macromolecule Content

Total Structure Weight: 26.52 kDa
Atom Count: 2,341
Modelled Residue Count: 230
Deposited Residue Count: 234
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	A	234	Paradendryphiella salina	Mutation(s): 1 Gene Names: PsAlg7C
UniProt
Find proteins for A0A7I9C8Z1 (Paradendryphiella salina) Explore A0A7I9C8Z1 Go to UniProtKB: A0A7I9C8Z1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7I9C8Z1
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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.141
R-Value Work: 0.115
R-Value Observed: 0.116
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.23	α = 74.74
b = 39.99	β = 78.48
c = 42.72	γ = 69.51

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: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Denmark	--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release

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.