6A39

The crystal structure of Mandelate oxidase Y128F with C4a-Malic acid-monooxide-FMN adduct

• PDB DOI: https://doi.org/10.2210/pdb6A39/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Amycolatopsis orientalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-06-15 Released: 2019-06-19 
• Deposition Author(s): Li, T.L., Lin, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

The crystal structure of Mandelate oxidase mutant Y128F with C4a-Malic acid-monooxide-FMN adduct

Li, T.L., Lin, K.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.63 kDa 
• Atom Count: 2,769 
• Modelled Residue Count: 330 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxymandelate oxidase	A	377	Amycolatopsis orientalis	Mutation(s): 1  Gene Names: hmo EC: 1.1.3.46
UniProt
Find proteins for O52792 (Amycolatopsis orientalis) Explore O52792  Go to UniProtKB:  O52792

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B8C	B [auth A]	(~{E})-2-[[(4~{a}~{S})-7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2~{S},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-5~{H}-benzo[g]pteridin-4~{a}-yl]oxy]-3-oxidanyl-but-2-enedioic acid C21 H25 N4 O15 P CYUZEIATLQOYCB-IVDAFHBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.44	α = 90
b = 138.44	β = 90
c = 109.144	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Li, T.L., Lin, K.H.

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description