8XBD | pdb_00008xbd

GH18 family chitinase from cold seep metagenome

• PDB DOI: https://doi.org/10.2210/pdb8XBD/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-06 Released: 2023-12-27 
• Deposition Author(s): Yang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

Literature

Exploring the role of organotrophic microbes in geochemical cycling of cold seep sediments.

Chen, Y., Yang, J., Huang, X., Zhang, J., Li, Q., Lyu, L., Ju, F., Li, J., Zhang, S.

(2025) Innov Geosci 3

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.64 kDa 
• Atom Count: 6,366 
• Modeled Residue Count: 776 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH18 chitinase-like superfamily protein	A [auth B], B [auth A]	405	uncultured bacterium	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for A0A142DUU5 (Klebsiella oxytoca) Explore A0A142DUU5  Go to UniProtKB:  A0A142DUU5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.278	α = 90
b = 114.286	β = 93.2
c = 110.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Yang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2025-04-30
  Changes: Database references, Structure summary