5JH8 | pdb_00005jh8

Crystal structure of chitinase from Chromobacterium violaceum ATCC 12472

• PDB DOI: https://doi.org/10.2210/pdb5JH8/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-04-20 Released: 2016-05-25 
• Deposition Author(s): Chang, C., Michalska, K., Tesar, C., Clancy, S., Joachimiak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.148 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of chitinase from Chromobacterium violaceum ATCC 12472

Chang, C., Michalska, K., Tesar, C., Clancy, S., Joachimiak, A.

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: 34.87 kDa 
• Atom Count: 3,113 
• Modeled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable chitinase	A	317	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: CV_2736
UniProt
Find proteins for Q7NUG2 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NUG2  Go to UniProtKB:  Q7NUG2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6KY	E [auth A]	(2S)-2-(dimethylamino)-4-(methylselanyl)butanoic acid C7 H15 N O2 Se HLLONANTKRYYCG-LURJTMIESA-N
HIS	F [auth A]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.148 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.03	α = 90
b = 67.034	β = 90.2
c = 57.301	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Chang, C., Michalska, K., Tesar, C., Clancy, S., Joachimiak, A.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Structure summary
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description