7WG0 | pdb_00007wg0

Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Heme Domain with N-palmitoyl-L-phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb7WG0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-12-27 Released: 2023-01-11 
• Deposition Author(s): Keita, O., Osami, S., Yuichiro, A., Hiroshi, S.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Heme Domain with N-palmitoyl-L-phenylalanine

Keita, O., Osami, S., Yuichiro, A., Hiroshi, S.

To be published.

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: 112.23 kDa 
• Atom Count: 7,835 
• Modeled Residue Count: 908 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	483	Priestia megaterium	Mutation(s): 1  Gene Names: BTA37_15100 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
MNH (Subject of Investigation/LOI)	D [auth A], F [auth B]	MANGANESE PROTOPORPHYRIN IX C34 H32 Mn N4 O4 UIBYYPDLEONCGQ-RGGAHWMASA-L
XPZ (Subject of Investigation/LOI)	C [auth A], E [auth B]	(2~{S})-2-(hexadecanoylamino)-3-phenyl-propanoic acid C25 H41 N O3 BAHIJPSQSKWCJX-QHCPKHFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.78	α = 90
b = 127.89	β = 90
c = 148.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Keita, O., Osami, S., Yuichiro, A., Hiroshi, S.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR15P3
Japan Society for the Promotion of Science (JSPS)	Japan	JP15H05806
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H04704
Japan Society for the Promotion of Science (JSPS)	Japan	JP19J21931

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description