4IED | pdb_00004ied

Crystal Structure of FUS-1 (OXA-85), a Class D beta-lactamase from Fusobacterium nucleatum subsp. polymorphum

PDB DOI: https://doi.org/10.2210/pdb4IED/pdb

Classification: HYDROLASE
Organism(s): Fusobacterium polymorphum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-13 Released: 2014-01-22
Deposition Author(s): Mangani, S., Benvenuti, M., Docquier, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.184 (Depositor), 0.190 (DCC)
R-Value Work:
0.146 (Depositor), 0.155 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of FUS-1 (OXA-85), a Class D beta-lactamase from Fusobacterium nucleatum subsp. polymorphum

Mangani, S., Benvenuti, M., Docquier, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 119.62 kDa
Atom Count: 10,027
Modeled Residue Count: 976
Deposited Residue Count: 1,016
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class D beta-lactamase	A, B, C, D	254	Fusobacterium polymorphum	Mutation(s): 0 Gene Names: fus1 EC: 3.5.2.6
UniProt
Find proteins for Q6XL56 (Fusobacterium nucleatum) Explore Q6XL56 Go to UniProtKB: Q6XL56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XL56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	H [auth A], I [auth A], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C]	E [auth A] F [auth A] K [auth B] L [auth B] M [auth B] E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.184 (Depositor), 0.190 (DCC)
R-Value Work: 0.146 (Depositor), 0.155 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.945	α = 84.59
b = 65.67	β = 82.91
c = 91.698	γ = 70.12

Software Package:

Software Name	Purpose
PXSOFT	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Mangani, S.

Benvenuti, M.

Docquier, J.D.

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary