3W6C

Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharide

• PDB DOI: https://doi.org/10.2210/pdb3W6C/pdb

• Classification: HYDROLASE
• Organism(s): Ralstonia sp. A-471
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-14 Released: 2013-05-15 
• Deposition Author(s): Arimori, T., Kawamoto, N., Okazaki, N., Nakazawa, M., Miyatake, K., Fukamizo, T., Ueda, M., Tamada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84.32 kDa 
• Atom Count: 5,220 
• Modelled Residue Count: 610 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme-like chitinolytic enzyme	A, B, C, D	183	Ralstonia sp. A-471	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for B7XCV4 (Ralstonia sp. A-471) Explore B7XCV4  Go to UniProtKB:  B7XCV4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I, J, K	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.041	α = 90
b = 99.041	β = 90
c = 242.143	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Arimori, T., Kawamoto, N., Okazaki, N., Nakazawa, M., Miyatake, K., Fukamizo, T., Ueda, M., Tamada, T.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary