6JS8

Structure of the CYP102A1 Haem Domain with N-Dehydroabietoyl-L-Tryptophan

• PDB DOI:  https://doi.org/10.2210/pdb6JS8/pdb

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


• Deposited: 2019-04-07 Released: 2020-03-18 
• Deposition Author(s): Stanfield, J.K., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y., Shoji, O.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.159 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain.

Stanfield, J.K., Omura, K., Matsumoto, A., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y., Shoji, O.

(2020) Angew Chem Int Ed Engl 59: 7611-7618

• PubMed: 32157795 
• DOI: https://doi.org/10.1002/anie.201913407
• Primary Citation of Related Structures:  
  6JLV, 6JMH, 6JMW, 6JO1, 6JS8, 6JVC, 6JZS, 6K24, 6K58, 6K9S


• PubMed Abstract: 
  

Despite CYP102A1 (P450BM3) representing one of the most extensively researched metalloenzymes, crystallisation of its haem domain upon modification can be a challenge. Crystal structures are indispensable for the efficient structure-based design of P450BM3 as a biocatalyst. The abietane diterpenoid derivative N-abietoyl-l-tryptophan (AbiATrp) is an outstanding crystallisation accelerator for the wild-type P450BM3 haem domain, with visible crystals forming within 2 hours and diffracting to a near-atomic resolution of 1.22 Å. Using these crystals as seeds in a cross-microseeding approach, an assortment of P450BM3 haem domain crystal structures, containing previously uncrystallisable decoy molecules and diverse artificial metalloporphyrins binding various ligand molecules, as well as heavily tagged haem-domain variants, could be determined. Some of the structures reported herein could be used as models of different stages of the P450BM3 catalytic cycle.

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Organizational Affiliation: 

Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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: 108.81 kDa 
• Atom Count: 8,816 
• Modelled Residue Count: 909 
• 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 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], O [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
C5R (Subject of Investigation/LOI)	E [auth A], Q [auth B]	(2S)-2-[[(1R,4aS,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,9,10,10a-hexahydrophenanthren-1-yl]carbonylamino]-3-(1H-indol-3-yl)propanoic acid C31 H38 N2 O3 WYAQKAIGBDDJPR-QKOWHPQASA-N
GOL	AA [auth B], BA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A], P [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.159 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.886	α = 90
b = 148.789	β = 98.42
c = 63.196	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Stanfield, J.K., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y., Shoji, O.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR15P3

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2020-05-06
  Changes: Database references