8BJR | pdb_00008bjr

Crystal structure of Paradendryphiella salina PL7C alginate lyase

PDB DOI: https://doi.org/10.2210/pdb8BJR/pdb

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

Deposited: 2022-11-06 Released: 2023-11-15
Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.150 (Depositor), 0.145 (DCC)
R-Value Work:
0.127 (Depositor), 0.124 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Paradendryphiella salina PL7C alginate lyase

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

To be published.

Macromolecule Content

Total Structure Weight: 25.83 kDa
Atom Count: 2,258
Modeled Residue Count: 230
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	234	Paradendryphiella salina	Mutation(s): 0 Gene Names: PsAlg7C
UniProt
Find proteins for A0A7I9C8Z1 (Paradendryphiella salina) Explore A0A7I9C8Z1 Go to UniProtKB: A0A7I9C8Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7I9C8Z1
Sequence Annotations Expand
Reference Sequence

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 D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.150 (Depositor), 0.145 (DCC)
R-Value Work: 0.127 (Depositor), 0.124 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.791	α = 73.63
b = 39.804	β = 76.353
c = 42.527	γ = 70.072

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
autoPROC	data processing
Coot	model building
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-15
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.