4AWU | pdb_00004awu

Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant in complex with para-chlorophenol

• PDB DOI: https://doi.org/10.2210/pdb4AWU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-06-05 Released: 2013-06-26 
• Deposition Author(s): Elegheert, J., Brige, A., Savvides, S.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.191 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Modulation of Isoalloxazine Ring Planarity Influences Fmn Electronic Properties in Old Yellow Enzymes

Elegheert, J., Pauwels, E., Wille, G., Brige, A., Savvides, S.N.

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: 40.91 kDa 
• Atom Count: 3,327 
• Modeled Residue Count: 364 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OXIDOREDUCTASE, FMN-BINDING	A	365	Shewanella oneidensis MR-1	Mutation(s): 1  EC: 1.6.99.1
UniProt
Find proteins for Q8EEC8 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EEC8  Go to UniProtKB:  Q8EEC8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PE4	G [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
4CH	D [auth A], E [auth A], F [auth A]	4-chlorophenol C6 H5 Cl O WXNZTHHGJRFXKQ-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.191 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.82	α = 90
b = 83.67	β = 90
c = 87.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Elegheert, J., Brige, A., Savvides, S.N.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description