4AWS | pdb_00004aws

Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant

• PDB DOI: https://doi.org/10.2210/pdb4AWS/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: 1.00 Å
• R-Value Free: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.120 (DCC) 
• R-Value Observed: 
  0.116 (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: 41.28 kDa 
• Atom Count: 3,662 
• Modeled Residue Count: 364 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYE1	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 5 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
BOG	D [auth A], E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
01F	F [auth A]	ethyl hydrogen carbonate C3 H6 O3 CQDGTJPVBWZJAZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.120 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.56	α = 90
b = 83.9	β = 90
c = 87.76	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	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: 2019-05-22
  Changes: Data collection, Derived calculations, Other, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-09
  Changes: Structure summary