5ZIS | pdb_00005zis

Crystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3

• PDB DOI: https://doi.org/10.2210/pdb5ZIS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-17 Released: 2018-08-15 
• Deposition Author(s): Omura, K., Aiba, Y., Onoda, H., Sugimoto, H., Shoji, O., Watanabe, Y.
• Funding Organization(s): Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Reconstitution of full-length P450BM3 with an artificial metal complex by utilising the transpeptidase Sortase A.

Omura, K., Aiba, Y., Onoda, H., Stanfield, J.K., Ariyasu, S., Sugimoto, H., Shiro, Y., Shoji, O., Watanabe, Y.

(2018) Chem Commun (Camb) 54: 7892-7895

• PubMed: 29845154 
• DOI: https://doi.org/10.1039/c8cc02760a
• Primary Citation Related Structures: 
  5ZIS, 5ZLH


• PubMed Abstract: 
  

  Haem substitution is an effective approach to tweak the function of haemoproteins. Herein, we report a facile haem substitution method for self-sufficient cytochrome P450BM3 (CYP102A1) from Bacillus megaterium utilising the transpeptidase Sortase A from Staphylococcus aureus. We successfully constructed Mn-substituted BM3 and investigated its catalytic activity.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 211.14 kDa 
• Atom Count: 14,722 
• Modeled Residue Count: 1,804 
• Deposited Residue Count: 1,820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B, C, D	455	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 0  Gene Names: cyp102A1, cyp102, BG04_163 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNH	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE PROTOPORPHYRIN IX C34 H32 Mn N4 O4 UIBYYPDLEONCGQ-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.76	α = 90
b = 155.32	β = 90
c = 208.98	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Omura, K., Aiba, Y., Onoda, H., Sugimoto, H., Shoji, O., Watanabe, Y.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR15P3
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17H03087

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description