3WSP

Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan

• PDB DOI: https://doi.org/10.2210/pdb3WSP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-20 Released: 2014-11-26 
• Deposition Author(s): Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Activation of Wild-type Cytochrome P450BM3 by the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence.

Cong, Z., Shoji, O., Kasai, C., Kawakami, N., Sugimoto, H., Shiro, Y., Watanabe, Y.

(2015) ACS Catal 5: 150-156

• DOI: https://doi.org/10.1021/cs501592f

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.29 kDa 
• Atom Count: 8,174 
• Modelled Residue Count: 906 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional P-450/NADPH-P450 reductase	A, B	456	Priestia megaterium	Mutation(s): 0  Gene Names: cyp102, cyp102A1, J04832.1 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W09	D [auth A], G [auth B]	N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan C20 H11 F17 N2 O3 HXHWGNOIRHNHBC-JTQLQIEISA-N
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DMS	E [auth A], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.875	α = 90
b = 145.392	β = 97.06
c = 63.029	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description