6KK8 | pdb_00006kk8

XN joint refinement of manganese catalase from Thermus Thermophilus HB27

• PDB DOI: https://doi.org/10.2210/pdb6KK8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Thermus thermophilus HB27
• Mutation(s): No 


• Deposited: 2019-07-24 Released: 2019-09-04 
• Deposition Author(s): Yamada, T., Yano, N., Kusaka, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.133 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.191 (Depositor) 
• R-Value Work: 
  0.152 (Depositor) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27

Yamada, T., Yano, N., Hosoya, T., Kusaka, K.

(2019) J Appl Crystallogr 

• DOI: https://doi.org/10.1107/S1600576719010239

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.23 kDa 
• Atom Count: 4,909 
• Modeled Residue Count: 599 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudocatalase	A, B	302	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1872 EC: 1.11.1.6
UniProt
Find proteins for Q72GH6 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GH6  Go to UniProtKB:  Q72GH6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN3	C [auth A], D [auth A], J [auth B], K [auth B]	MANGANESE (III) ION Mn MMIPFLVOWGHZQD-UHFFFAOYSA-N
O	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.133 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.191 (Depositor) 
• R-Value Work:  0.152 (Depositor) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.396	α = 90
b = 133.396	β = 90
c = 133.396	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Yamada, T., Yano, N., Kusaka, K.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description