4MB3

Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella marina

• PDB DOI: https://doi.org/10.2210/pdb4MB3/pdb

• Classification: HYDROLASE
• Organism(s): Moritella marina
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-19 Released: 2014-03-19 
• Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.183 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution

Malecki, P.H., Vorgias, C.E., Petoukhov, M.V., Svergun, D.I., Rypniewski, W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 676-684

• PubMed: 24598737 
• DOI: https://doi.org/10.1107/S1399004713032264
• Primary Citation of Related Structures:  
  4MB3, 4MB4, 4MB5


• PubMed Abstract: 
  

  The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, but only a few have been solved. The flexibility of the hinge regions between the domains apparently makes these proteins difficult to crystallize. The analysis of an active-site mutant of MmChi60 in an unliganded form and in complex with the substrates NAG4 and NAG5 revealed significant differences in the substrate-binding site compared with the previously determined complexes of most studied chitinases. A SAXS experiment demonstrated that in addition to the elongated state found in the crystal, the protein can adapt other conformations in solution ranging from fully extended to compact.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.01 kDa 
• Atom Count: 5,137 
• Modelled Residue Count: 528 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase 60	A	528	Moritella marina	Mutation(s): 1  Gene Names: chi60 EC: 3.2.1.14
UniProt
Find proteins for B1VBB0 (Moritella marina) Explore B1VBB0  Go to UniProtKB:  B1VBB0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GLY	F [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
IMD	H [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A], C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.183 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.657	α = 90
b = 67.657	β = 90
c = 255.643	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Malecki, P.H., Vorgias, C.E., Rypniewski, W.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description