5XEM | pdb_00005xem

Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base

PDB DOI: https://doi.org/10.2210/pdb5XEM/pdb

Classification: TRANSFERASE
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-05 Released: 2018-04-11
Deposition Author(s): Kezuka, Y., Yoshida, Y., Nonaka, T.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base

Kezuka, Y., Yoshida, Y., Nonaka, T.

To be published.

Macromolecule Content

Total Structure Weight: 69.38 kDa
Atom Count: 5,174
Modelled Residue Count: 603
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A, B	310	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: FN1220 EC: 2.5.1.47
UniProt
Find proteins for Q8RE94 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RE94 Go to UniProtKB: Q8RE94
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RE94
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B]	D [auth A], P [auth B], R [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain P [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B] Focus chain R [auth B]
85F Query on 85F Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	(2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid C₆ H₁₂ N₂ O₄ S DWPCPZJAHOETAG-IMJSIDKUSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
PG5 Query on PG5 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth B]	M [auth A], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B]	E [auth A], F [auth A], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth B]
CA Query on CA 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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]