4MB4

Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.481 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


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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.,Sect.D 70: 676-684

  • DOI: 10.1107/S1399004713032264
  • Primary Citation of Related Structures:  4MB3, 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 o ...

    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.


    Related Citations: 
    • Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium
      Malecki, P.H.,Raczynska, J.E.,Vorgias, C.E.,Rypniewski, W.
      (2013) Acta Crystallogr.,Sect.D 69: 821


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase 60
A
528Moritella marinaGene Names: chi60
EC: 3.2.1.14
Find proteins for B1VBB0 (Moritella marina)
Go to UniProtKB:  B1VBB0
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

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A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.481 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.134 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 67.318α = 90.00
b = 67.318β = 90.00
c = 255.764γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release