4TX8

Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb4TX8/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-07-02 Released: 2015-10-14 
• Deposition Author(s): Pereira, H.M., Lobo, M.D.P., Brandao-Neto, J., Grangeiro, T.B.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq), Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.8 kDa 
• Atom Count: 3,133 
• Modelled Residue Count: 374 
• Deposited Residue Count: 439 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable chitinase A	A	439	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: CV_2935
UniProt
Find proteins for Q7NTW8 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NTW8  Go to UniProtKB:  Q7NTW8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC	E [auth A], F [auth A], G [auth A], H [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.48	α = 90
b = 120.48	β = 90
c = 106.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
xia2	data scaling
PHASER	phasing
GDA	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Pereira, H.M., Lobo, M.D.P., Brandao-Neto, J., Grangeiro, T.B.

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Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	--
Sao Paulo Research Foundation (FAPESP)	Brazil	--

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description
• Version 1.2: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary