6PT7 | pdb_00006pt7

Structure of KatE1 catalase from Acinetobacter sp. Ver3

• PDB DOI: https://doi.org/10.2210/pdb6PT7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter sp. Ver3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-15 Released: 2020-07-22 
• Deposition Author(s): Gonzalez, J.M., Sartorio, M.G., Cortez, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.209 (Depositor) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina

Sartorio, M.G., Cortez, N., Gonzalez, J.M.

(2021) Acta Crystallogr D Biol Crystallogr D77: 369-379

• DOI: https://doi.org/10.1107/S2059798321000929

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 58.16 kDa 
• Atom Count: 4,345 
• Modeled Residue Count: 500 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A	500	Acinetobacter sp. Ver3	Mutation(s): 0  Gene Names: CL42_01515

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMT	A	L-PEPTIDE LINKING	C5 H11 N O4 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.209 (Depositor) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.538	α = 90
b = 112.538	β = 90
c = 314.634	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Gonzalez, J.M., Sartorio, M.G., Cortez, N.

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary