1JKV

Crystal Structure of Manganese Catalase from Lactobacillus plantarum complexed with azide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of manganese catalase from Lactobacillus plantarum.

Barynin, V.V.Whittaker, M.M.Antonyuk, S.V.Lamzin, V.S.Harrison, P.M.Artymiuk, P.J.Whittaker, J.W.

(2001) Structure 9: 725-738

  • DOI: 10.1016/s0969-2126(01)00628-1
  • Primary Citation of Related Structures:  
    1JKV, 1JKU

  • PubMed Abstract: 
  • Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and the other, a structurally distinct family containing nonheme manganese ...

    Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and the other, a structurally distinct family containing nonheme manganese. We have solved the structure of the mesophilic manganese catalase from Lactobacillus plantarum and its azide-inhibited complex.


    Organizational Affiliation

    The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, United Kingdom. v.barynin@sheffield.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pseudocatalaseA, B, C, D, E, F266Lactiplantibacillus plantarumMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P60355 (Lactiplantibacillus plantarum)
Explore P60355 
Go to UniProtKB:  P60355
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth E] , FA [auth C] , GA [auth C] , HA [auth C] , IB [auth F] , JB [auth F] , KB [auth F] , N [auth A] , 
AB [auth E],  FA [auth C],  GA [auth C],  HA [auth C],  IB [auth F],  JB [auth F],  KB [auth F],  N [auth A],  O [auth A],  P [auth A],  PA [auth D],  QA [auth D],  X [auth B],  YA [auth E],  ZA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN3
Query on MN3

Download Ideal Coordinates CCD File 
DA [auth C] , EA [auth C] , GB [auth F] , HB [auth F] , L [auth A] , M [auth A] , NA [auth D] , OA [auth D] , 
DA [auth C],  EA [auth C],  GB [auth F],  HB [auth F],  L [auth A],  M [auth A],  NA [auth D],  OA [auth D],  V [auth B],  W [auth B],  WA [auth E],  XA [auth E]
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download Ideal Coordinates CCD File 
CA [auth C], FB [auth F], K [auth A], MA [auth D], U [auth B], VA [auth E]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BB [auth F], G [auth A], IA [auth D], Q [auth B], RA [auth E], Y [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CB [auth F] , DB [auth F] , EB [auth F] , H [auth A] , I [auth A] , J [auth A] , 
AA [auth C],  BA [auth C],  CB [auth F],  DB [auth F],  EB [auth F],  H [auth A],  I [auth A],  J [auth A],  JA [auth D],  KA [auth D],  LA [auth D],  R [auth B],  S [auth B],  SA [auth E],  T [auth B],  TA [auth E],  UA [auth E],  Z [auth C]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.21α = 90
b = 95.55β = 106.18
c = 106.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-12-14
    Changes: Structure summary