8W1K

Crystal Structure of a fatty acid decarboxylase from Corynebacterium lipophiloflavum in complex with oleic acid

PDB DOI: https://doi.org/10.2210/pdb8W1K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium lipophiloflavum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-16 Released: 2024-12-04
Deposition Author(s): Generoso, W.C., Miyamoto, R.Y., Murakami, M.T., Zanphorlin, L.M.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197
R-Value Work: 0.168
R-Value Observed: 0.170

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Coordinated conformational changes play a pivotal role in unsaturated fatty acid decarboxylation into renewable olefin

Generoso, W.C., Alvarenga, A.H.S., Simoes, I.T., Miyamoto, R.Y., Mandelli, F., Santos, C.A., Santos, C.R., Colombari, F.M., Morais, M.A.B., Fernandes, R., Persinoti, G.F., Murakami, M.T., Zanphorlin, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 152.12 kDa
Atom Count: 11,022
Modelled Residue Count: 1,259
Deposited Residue Count: 1,350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid decarboxylase	A, B, C	450	Corynebacterium lipophiloflavum	Mutation(s): 0 Gene Names: HMPREF0298_0515
UniProt
Find proteins for C0XPZ5 (Corynebacterium lipophiloflavum (strain ATCC 700352 / DSM 44291 / CCUG 37336 / JCM 10383 / DMMZ 1944)) Explore C0XPZ5 Go to UniProtKB: C0XPZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0XPZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C]	D [auth A], L [auth B], R [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain L [auth B] Focus chain R [auth C]
OLA (Subject of Investigation/LOI) Query on OLA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C]	E [auth A], M [auth B], S [auth C]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	K [auth A], Q [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C]	F [auth A], N [auth B], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C]	G [auth A] H [auth A] I [auth A] O [auth B] P [auth B] G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C] mmCIF format, chain J [auth A] mmCIF format, chain V [auth C]	J [auth A], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.905	α = 90
b = 170.367	β = 90
c = 121.603	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2018/02865-2
Sao Paulo Research Foundation (FAPESP)	Brazil	2019/08855-1
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/14410-2