9WHD | pdb_00009whd

Crystal Structure of a GH167 Enzyme from Wenyingzhuangia aestuarii

PDB DOI: https://doi.org/10.2210/pdb9WHD/pdb

Classification: HYDROLASE
Organism(s): Wenyingzhuangia aestuarii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-08-26 Released: 2025-10-01
Deposition Author(s): Chen, F., Chang, Y.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.269 (Depositor), 0.256 (DCC)
R-Value Work:
0.217 (Depositor)
R-Value Observed:
0.218 (Depositor)

Starting Model: in silico
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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

A carrageenase from Wenyingzhuangia aestuarii reveals a novel cleavage pattern for the GH167 family

Chen, F., Xue, C., Guan, Q., Sun, M., Zhang, Z., Chen, G., Chang, Y.

(2026) Algal Res 99: 104975

DOI: https://doi.org/10.1016/j.algal.2026.104975

Macromolecule Content

Total Structure Weight: 195.28 kDa
Atom Count: 12,878
Modeled Residue Count: 1,479
Deposited Residue Count: 1,710
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH167 glycoside hydrolase	A, B	855	Wenyingzhuangia aestuarii	Mutation(s): 0 EC: 3.2.1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.269 (Depositor), 0.256 (DCC)
R-Value Work: 0.217 (Depositor)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.623	α = 90
b = 113.341	β = 90
c = 241.804	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2023YFD2100605

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release
Version 1.1: 2026-11-04
Changes: Database references