5B2V | pdb_00005b2v

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

• PDB DOI: https://doi.org/10.2210/pdb5B2V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-03 Released: 2017-02-08 
• Deposition Author(s): Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.
• Funding Organization(s): The Ministry of Education, Culture, Sports, Science, and Technology, The Japan Science and Technology Agency (JST)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of P450BM3 with decoy molecules

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

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 106.83 kDa 
• Atom Count: 7,600 
• Modeled Residue Count: 906 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	456	Priestia megaterium	Mutation(s): 0  Gene Names: cyp102A1, cyp102 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
W06	D [auth A], F [auth B]	(2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,6-undecakis(fluoranyl)hexanoylamino]propanoic acid C17 H11 F11 N2 O3 HOHTXGBLBJYLPP-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.881	α = 90
b = 147.491	β = 98.23
c = 64.247	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.

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Funding Organization	Location	Grant Number
The Ministry of Education, Culture, Sports, Science, and Technology	Japan	24225004
The Ministry of Education, Culture, Sports, Science, and Technology	Japan	15H05806
The Japan Science and Technology Agency (JST)	Japan	15658843

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description