3CY1 | pdb_00003cy1

Crystal structure of the cytochrome P450 CYP121 S279A mutant from M. tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3CY1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-04-25 Released: 2008-09-23 
• Deposition Author(s): Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.211 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Characterisation of active site of cytochrome P450 CYP121

McLean, K.J., Carrol, P., Lewis, D.G., Dunford, A.J., Seward, H.E., Neeli, R., Cole, S.T., Leys, D., Parish, T., Munro, A.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.19 kDa 
• Atom Count: 3,553 
• Modeled Residue Count: 395 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	396	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: cyp121 EC: 1.14 (PDB Primary Data), 1.14.19.70 (UniProt)
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	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.211 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.67	α = 90
b = 77.67	β = 90
c = 263.503	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): Leys, D.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description