4W5U

Crystal structure of chitinase 40 from thermophilic bacteria Streptomyces thermoviolaceus.

• PDB DOI: https://doi.org/10.2210/pdb4W5U/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces thermoviolaceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-18 Released: 2015-08-26 
• Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.
• Funding Organization(s): The project was co-funded by the European Union within the European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.208 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Starting Model: other

Literature

The Crystal Structure of a Streptomyces thermoviolaceus Thermophilic Chitinase Known for Its Refolding Efficiency

Malecki, P.H., Bejger, M., Rypniewski, W., Vorgias, C.E.

(2020) Int J Mol Sci 

• DOI: https://doi.org/10.3390/ijms21082892

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 86.87 kDa 
• Atom Count: 5,660 
• Modelled Residue Count: 739 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A [auth B], B [auth A]	408	Streptomyces thermoviolaceus	Mutation(s): 0  Gene Names: chi40 EC: 3.2.1.14
UniProt
Find proteins for Q56077 (Streptomyces thermoviolaceus) Explore Q56077  Go to UniProtKB:  Q56077

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth B], D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.208 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.15	α = 90
b = 183.15	β = 90
c = 130.814	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.

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Funding Organization	Location	Grant Number
The project was co-funded by the European Union within the European Regional Development Fund	Poland	--

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-04-29
  Changes: Atomic model, Database references
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description