1UB2 | pdb_00001ub2

Crystal structure of catalase-peroxidase from Synechococcus PCC 7942

• PDB DOI: https://doi.org/10.2210/pdb1UB2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-28 Released: 2004-03-28 
• Deposition Author(s): Wada, K., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.232 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of catalase-peroxidase from Synechococcus PCC 7942

Wada, K., Tada, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 80.62 kDa 
• Atom Count: 6,243 
• Modeled Residue Count: 700 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A	720	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  EC: 1.11.1.6 (PDB Primary Data), 1.11.1.21 (UniProt)
UniProt
Find proteins for Q31MN3 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31MN3  Go to UniProtKB:  Q31MN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.232 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.208	α = 90
b = 109.208	β = 90
c = 202.661	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-28 
Deposition Author(s): Wada, K., Tada, T.

Revision History  

• Version 1.0: 2004-03-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary