4MB5

Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.639 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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

    Hamburg Unit, EMBL c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany.,Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Zografou Campus, 157 01 Athens, Greece.,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 marinaMutation(s): 1 
Gene Names: chi60
EC: 3.2.1.14
Find proteins for B1VBB0 (Moritella marina)
Go to UniProtKB:  B1VBB0
Small Molecules
Ligands 7 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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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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A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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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: 1.639 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 67.057α = 90.00
b = 67.057β = 90.00
c = 256.633γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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