3L5A | pdb_00003l5a

Crystal structure of a probable NADH-dependent flavin oxidoreductase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3L5A/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus JH1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-21 Released: 2010-12-22 
• Deposition Author(s): Lam, R., Gordon, R.D., Vodsedalek, J., Battaile, K.P., Grebemeskel, S., Lam, K., Romanov, V., Chan, T., Mihajlovic, V., Thompson, C.M., Guthrie, J., Pai, E.F., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.183 (DCC) 

Literature

Crystal structure of a probable NADH-dependent flavin oxidoreductase from Staphylococcus aureus

Lam, R., Gordon, R.D., Vodsedalek, J., Battaile, K.P., Grebemeskel, S., Lam, K., Romanov, V., Chan, T., Mihajlovic, V., Thompson, C.M., Guthrie, J., Pai, E.F., Chirgadze, N.Y.

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)

Macromolecule Content 

• Total Structure Weight: 48 kDa 
• Atom Count: 3,303 
• Modeled Residue Count: 381 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH/flavin oxidoreductase/NADH oxidase	A	419	Staphylococcus aureus subsp. aureus JH1	Mutation(s): 0  Gene Names: SaurJH1_0381

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A], C [auth A], D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.183 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.941	α = 90
b = 75.342	β = 90
c = 80.736	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Lam, R., Gordon, R.D., Vodsedalek, J., Battaile, K.P., Grebemeskel, S., Lam, K., Romanov, V., Chan, T., Mihajlovic, V., Thompson, C.M., Guthrie, J., Pai, E.F., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary