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

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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

Literature

Expression, Purification, and Structure Analysis of the Catalytic Domain of a GH167 Enzyme from Wenyingzhuangia aestuarii

Chen, F., Chang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

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

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

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Chen, F., Chang, Y.

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Funding Organization	Location	Grant Number
Other government	China	2023YFD2100605

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release