6MLY | pdb_00006mly

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 (Depositor), 0.261 (DCC)
R-Value Work:
0.220 (Depositor), 0.211 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 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
Modeled Residue Count: 3,029
Deposited Residue Count: 3,228
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 G [auth A] SDF format, chain J [auth B] SDF format, chain M [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] SDF format, chain N [auth C] SDF 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 Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain N [auth C] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain N [auth C] mmCIF format, chain F [auth A]	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 I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain E [auth A]	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 H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF 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 (Depositor), 0.261 (DCC)
R-Value Work: 0.220 (Depositor), 0.211 (DCC)
R-Value Observed: 0.222 (Depositor)

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

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View more in-depth experimental data

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
Version 1.3: 2024-10-23
Changes: Structure summary