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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the Epsilon-Lysine Oxidase from Marinomonas Mediterranea

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2JXJ3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain WB [auth B] SDF format, chain XB [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain XB [auth B] mmCIF format, chain WB [auth B] mmCIF format, chain XB [auth B]	WB [auth B], XB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain WB [auth B] Focus chain XB [auth B] Interactions & Density Focus chain WB [auth B] Focus chain XB [auth B]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth B] SDF format, chain Z [auth A] SDF format, chain ZB [auth B] SDF format, chain P [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth B] MOL2 format, chain P [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain UB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain YB [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth B] mmCIF format, chain P [auth A] mmCIF format, chain ZA [auth B]	AA [auth A] AB [auth B] AC [auth B] BA [auth A] BB [auth B] 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		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B]	C [auth A], D [auth A], VA [auth B], WA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain VA [auth B] Focus chain WA [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Medrano, F.J.

Romero, A.

Revision History (Full details and data files)

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