1IO9 | pdb_00001io9

THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION STRUCTURAL ORIGIN OF ITS THERMOSTABILITY AND FUNCTIONAL PROPERTIES

• PDB DOI: https://doi.org/10.2210/pdb1IO9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-02-08 Released: 2001-03-07 
• Deposition Author(s): Park, S.-Y., Yamane, K., Adachi, S., Shiro, Y., Sligar, S.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.284 (Depositor) 
• R-Value Work: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties.

Park, S.Y., Yamane, K., Adachi, S., Shiro, Y., Weiss, K.E., Maves, S.A., Sligar, S.G.

(2002) J Inorg Biochem 91: 491-501

• PubMed: 12237217 
• DOI: https://doi.org/10.1016/s0162-0134(02)00446-4
• Primary Citation Related Structures: 
  1IO7, 1IO8, 1IO9


• PubMed Abstract: 
  

  Crystal structures of a thermostable cytochrome P450 (CYP119) and a site-directed mutant, (Phe24Leu), from the acidothermophilic archaea Sulfolobus solfataricus were determined at 1.5-2.0 A resolution. We identify important crystallographic waters in the ferric heme pocket, observe protein conformational changes upon inhibitor binding, and detect a unique distribution of surface charge not found in other P450s. An analysis of factors contributing to thermostability of CYP119 of these high resolution structures shows an apparent increase in clustering of aromatic residues and optimum stacking. The contribution of aromatic stacking was investigated further with the mutant crystal structure and differential scanning calorimetry.

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Organizational Affiliation: 
• RIKEN Harima Institute/Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.08 kDa 
• Atom Count: 6,127 
• Modeled Residue Count: 720 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 CYP119	A, B	368	Saccharolobus solfataricus	Mutation(s): 0  EC: 1.14.14 (PDB Primary Data), 1.14 (UniProt), 1.11.1.7 (UniProt)
UniProt
Find proteins for Q55080 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q55080  Go to UniProtKB:  Q55080

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.284 (Depositor) 
• R-Value Work:  0.227 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.587	α = 90
b = 87.587	β = 90
c = 223.151	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-07 
Deposition Author(s): Park, S.-Y., Yamane, K., Adachi, S., Shiro, Y., Sligar, S.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2001-03-07
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description