6UPI | pdb_00006upi

Crystal structure of Mycobacterium tuberculosis CYP121 bound with a hydroxylated intermediate of cYF-4-OMe

• PDB DOI: https://doi.org/10.2210/pdb6UPI/pdb

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


• Deposited: 2019-10-17 Released: 2020-04-29 
• Deposition Author(s): Nguyen, R.C.D., Yang, Y., Liu, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Substrate-Assisted Hydroxylation and O-Demethylation in the Peroxidase-like Cytochrome P450 Enzyme CYP121

Nguyen, R.C., Yang, Y., Davis, I., Liu, A.

(2020) ACS Catal 10: 1628-1639

• DOI: https://doi.org/10.1021/acscatal.9b04596

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

Macromolecule Content 

• Total Structure Weight: 44.15 kDa 
• Atom Count: 3,440 
• Modeled Residue Count: 395 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycocyclosin synthase	A	395	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: cyp121, MT2336 EC: 1.14.19.70
UniProt
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPP7  Go to UniProtKB:  P9WPP7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
QFD (Subject of Investigation/LOI)	C [auth A]	(3S,6S)-3-{[4-(hydroxymethoxy)phenyl]methyl}-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione C19 H20 N2 O5 XYLVFIWANSQWOX-IRXDYDNUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.37	α = 90
b = 77.37	β = 90
c = 261.973	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Currently 6UPI does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Nguyen, R.C.D., Yang, Y., Liu, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM108988

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description