4TT5 | pdb_00004tt5

Crystal Structure of CYP119 from Sulfolobus acidocaldarius, complexed with 4-(4-bromophenyl)-1H imidazole

• PDB DOI: https://doi.org/10.2210/pdb4TT5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfolobus acidocaldarius DSM 639
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-19 Released: 2015-02-18 
• Deposition Author(s): Madrona, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

NMR and X-ray Analysis of CYP119 ligand-dependent conformational changes

Basudhar, D., Madrona, Y., Ortiz de Montellano, P.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.86 kDa 
• Atom Count: 3,290 
• Modeled Residue Count: 367 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 119	A	368	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0  Gene Names: cyp119, Saci_2081 EC: 1.14 (PDB Primary Data), 1.11.1.7 (PDB Primary Data)
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 3 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
36Y	C [auth A]	4-(4-bromophenyl)-1H-imidazole C9 H7 Br N2 YLIOAWKNPLJMID-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.34	α = 90
b = 165.34	β = 90
c = 76.81	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Madrona, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description