2HAY | pdb_00002hay

The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS

• PDB DOI: https://doi.org/10.2210/pdb2HAY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-13 Released: 2006-07-04 
• Deposition Author(s): Kim, Y., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS

Kim, Y., Duggan, E., Clancy, S., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.25 kDa 
• Atom Count: 8,080 
• Modeled Residue Count: 876 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NAD(P)H-flavin oxidoreductase	A, B, C, D	224	Streptococcus pyogenes serotype M1	Mutation(s): 7  EC: 1
UniProt
Find proteins for Q9A120 (Streptococcus pyogenes serotype M1) Explore Q9A120  Go to UniProtKB:  Q9A120

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	F [auth A], I [auth B], J [auth C], M [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	E [auth A], G [auth B], H [auth B], K [auth D], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.205	α = 90
b = 91.874	β = 90
c = 175.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Kim, Y., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary