3D1C | pdb_00003d1c

Crystal structure of Flavin-containing Putative Monooxygenase (NP_373108.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D1C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-05 Released: 2008-05-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50.

Hwang, W.C., Xu, Q., Wu, B., Godzik, A.

(2014) Proteins 

• DOI: https://doi.org/10.1002/prot.24661

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.81 kDa 
• Atom Count: 2,972 
• Modeled Residue Count: 358 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-containing Putative Monooxygenase	A	369	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: NP_373108.1, SAV2584 EC: 1
UniProt
Find proteins for Q99R54 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99R54  Go to UniProtKB:  Q99R54

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNL	G [auth A]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.40 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33D1C

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.247	α = 90
b = 109.247	β = 90
c = 87.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2014-08-20
  Changes: Database references
• Version 1.3: 2015-12-23
  Changes: Database references
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.7: 2024-10-30
  Changes: Data collection, Structure summary