3QGP | pdb_00003qgp

Crystal structure of IsdI in complex with heme and cyanide

• PDB DOI: https://doi.org/10.2210/pdb3QGP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-24 Released: 2011-07-20 
• Deposition Author(s): Ukpabi, G.N., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Heme Ruffling Enables the Catalytic Activity of the Heme Degrading Enzyme IsdI

Takayama, S.J., Ukpabi, G.N., Murphy, M.E.P., Mauk, A.G.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.36 kDa 
• Atom Count: 2,246 
• Modeled Residue Count: 220 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-degrading monooxygenase isdI	A, B	110	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0  Gene Names: isdI, SA0160 EC: 1.14.99.3 (PDB Primary Data), 1.14.99.48 (UniProt)
UniProt
Find proteins for Q7A827 (Staphylococcus aureus (strain N315)) Explore Q7A827  Go to UniProtKB:  Q7A827

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	D [auth A], F [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N
MG	G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 65.86	β = 90
c = 69.33	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Ukpabi, G.N., Murphy, M.E.P.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description