6MLY

Bifunctional GH43-CE Bacteroides eggerthii, BACEGG_01304

PDB DOI: https://doi.org/10.2210/pdb6MLY/pdb

Classification: HYDROLASE
Organism(s): Bacteroides eggerthii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-09-28 Released: 2019-10-02
Deposition Author(s): Koropatkin, N.M., Pereira, G.V., Cann, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269
R-Value Work: 0.220
R-Value Observed: 0.222

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Degradation of complex arabinoxylans by human colonic Bacteroidetes

Pereira, G.V., DAlessandro-Gabazza, C., Farris, J., Wefers, D., Mackie, R., Koropatkin, N.M., Gabazza, E.C., Cann, I.

(2021) Nat Commun

DOI: https://doi.org/10.1038/s41467-020-20737-5

Macromolecule Content

Total Structure Weight: 360.05 kDa
Atom Count: 24,144
Modelled Residue Count: 3,029
Deposited Residue Count: 3,228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional GH43-CE protein	A, B, C, D	807	Bacteroides eggerthii	Mutation(s): 0 Gene Names: xynB_2, NCTC11155_00458 EC: 3.2.1.37
UniProt
Find proteins for E5WZQ7 (Bacteroides eggerthii 1_2_48FAA) Explore E5WZQ7 Go to UniProtKB: E5WZQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E5WZQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	F [auth A] G [auth A] J [auth B] M [auth C] N [auth C] F [auth A], G [auth A], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C]	E [auth A], I [auth B], L [auth C], P [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain U [auth D]	H [auth A], K [auth B], O [auth C], U [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269
R-Value Work: 0.220
R-Value Observed: 0.222
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 254.734	α = 90
b = 93.31	β = 123.38
c = 214.039	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MrBUMP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-10-02

Deposition Author(s):

Koropatkin, N.M.

Pereira, G.V.

Cann, I.

Revision History (Full details and data files)

Version 1.0: 2019-10-02
Type: Initial release
Version 1.1: 2021-01-27
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description