6LDU | pdb_00006ldu

Crystal structure of CeCht1, a nematode I family chitinase from C. elegans

• PDB DOI: https://doi.org/10.2210/pdb6LDU/pdb

• Classification: HYDROLASE
• Organism(s): Caenorhabditis elegans
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2019-11-23 Released: 2021-05-26 
• Deposition Author(s): Chen, Q., Yang, Q., Zhou, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CeCht1, a nematode I family chitinase from C. elegans

Chen, Q., Yang, Q., Zhou, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.78 kDa 
• Atom Count: 3,513 
• Modeled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endochitinase	A	383	Caenorhabditis elegans	Mutation(s): 0  Gene Names: cht-1, C04F6.3 EC: 3.2.1.14
UniProt
Find proteins for Q11174 (Caenorhabditis elegans) Explore Q11174  Go to UniProtKB:  Q11174
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.571	α = 90
b = 66.935	β = 102.709
c = 57.352	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Chen, Q., Yang, Q., Zhou, Y.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary