2YMW | pdb_00002ymw

Structure of the epsilon-lysine oxidase from Marinomonas mediterranea

• PDB DOI: https://doi.org/10.2210/pdb2YMW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Marinomonas mediterranea MMB-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-10 Released: 2013-10-23 
• Deposition Author(s): Medrano, F.J., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.279 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Structure of the Epsilon-Lysine Oxidase from Marinomonas Mediterranea

Medrano, F.J., Sanchez-Amat, A., Romero, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 169.85 kDa 
• Atom Count: 11,836 
• Modeled Residue Count: 1,365 
• Deposited Residue Count: 1,492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LYSINE 6-OXIDASE	A, B	746	Marinomonas mediterranea MMB-1	Mutation(s): 0  EC: 1.4.3.20
UniProt
Find proteins for F2JXJ3 (Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1)) Explore F2JXJ3  Go to UniProtKB:  F2JXJ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	WB [auth B], XB [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH	AA [auth A], AB [auth B], AC [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], E [auth A], EA [auth A], EB [auth B], F [auth A], FA [auth A], FB [auth B], G [auth A], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], NB [auth B], O [auth A], OA [auth A], OB [auth B], P [auth A], PA [auth A], PB [auth B], Q [auth A], QA [auth A], QB [auth B], R [auth A], RA [auth A], RB [auth B], S [auth A], SA [auth A], SB [auth B], T [auth A], TA [auth A], TB [auth B], U [auth A], UA [auth A], UB [auth B], V [auth A], VB [auth B], W [auth A], X [auth A], XA [auth B], Y [auth A], YA [auth B], YB [auth B], Z [auth A], ZA [auth B], ZB [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
NA	C [auth A], D [auth A], VA [auth B], WA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ	A, B	L-PEPTIDE LINKING	C11 H10 N2 O4		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.279 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.68	α = 90
b = 127.883	β = 107.18
c = 106.897	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Medrano, F.J., Romero, A.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Source and taxonomy
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary