9IRQ | pdb_00009irq

Alginate lyase (Microbulbifer sp. ALW1)

PDB DOI: https://doi.org/10.2210/pdb9IRQ/pdb

Classification: HYDROLASE
Organism(s): Microbulbifer sp. ALW1
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-07-16 Released: 2025-01-22
Deposition Author(s): Zhu, Y.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.239 (Depositor), 0.238 (DCC)
R-Value Work:
0.188 (Depositor), 0.192 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Molecular cloning and characterization of AlgL17, a new exo-oligoalginate lyase from Microbulbifer sp. ALW1

Zhu, Y.B.

To be published.

Macromolecule Content

Total Structure Weight: 157.59 kDa
Atom Count: 11,464
Modeled Residue Count: 1,414
Deposited Residue Count: 1,414
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase AlgL17	A, B	707	Microbulbifer sp. ALW1	Mutation(s): 0 Gene Names: algl17 EC: 4.2.2.3
UniProt
Find proteins for A0ACD6B903 (Microbulbifer sp. (strain ALW1)) Explore A0ACD6B903 Go to UniProtKB: A0ACD6B903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B903
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.239 (Depositor), 0.238 (DCC)
R-Value Work: 0.188 (Depositor), 0.192 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.108	α = 90
b = 90.421	β = 110.01
c = 88.287	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	No. 22178142

Revision History (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release

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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.