5HIW

Sorangium cellulosum So Ce56 cytochrome P450 260B1

• PDB DOI: https://doi.org/10.2210/pdb5HIW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sorangium cellulosum So ce56
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-12 Released: 2016-08-03 
• Deposition Author(s): Salamanca-Pinzon, S.G., Carius, Y., Khatri, Y., Bernhardt, R., Lancaster, C.R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure-function analysis for the hydroxylation of Delta 4 C21-steroids by the myxobacterial CYP260B1.

Salamanca-Pinzon, S.G., Khatri, Y., Carius, Y., Keller, L., Muller, R., Lancaster, C.R., Bernhardt, R.

(2016) FEBS Lett 590: 1838-1851

• PubMed: 27177597 
• DOI: https://doi.org/10.1002/1873-3468.12217
• Primary Citation of Related Structures:  
  5HIW


• PubMed Abstract: 
  

  Myxobacterial CYP260B1 from Sorangium cellulosum was heterologously expressed in Escherichia coli and purified. The in vitro conversion of a small focused substrate library comprised of Δ4 C21-steroids and steroidal drugs using surrogate bovine redox partners shows that CYP260B1 is a novel steroid hydroxylase. CYP260B1 performs the regio- and stereoselective hydroxylation of the glucocorticoid cortodoxone (RSS) to produce 6β-OH-RSS. The substrate-free crystal structure of CYP260B1 (PDB 5HIW) was resolved. Docking of the tested ligands into the crystal structure suggested that the C17 hydroxy moiety and the presence of either a keto or a hydroxy group at C11 determine the selectivity of hydroxylation.

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Organizational Affiliation: 

Institute of Biochemistry, Saarland University, Saarbrücken, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 44.21 kDa 
• Atom Count: 3,364 
• Modelled Residue Count: 391 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 CYP260B1	A	398	Sorangium cellulosum So ce56	Mutation(s): 0  Gene Names: cypA3, sce4806 EC: 1.14
UniProt
Find proteins for A9FFA1 (Sorangium cellulosum (strain So ce56)) Explore A9FFA1  Go to UniProtKB:  A9FFA1

Small Molecules

Ligands 2 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
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.42	α = 90
b = 60.42	β = 90
c = 190.82	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Salamanca-Pinzon, S.G., Carius, Y., Khatri, Y., Bernhardt, R., Lancaster, C.R.D.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description