6FWL

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex alpha-Glc-1,3-(1,2-anhydro-carba-mannose)

PDB DOI: https://doi.org/10.2210/pdb6FWL/pdb

Classification: HYDROLASE
Organism(s): Bacteroides xylanisolvens XB1A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-06 Released: 2019-09-18
Deposition Author(s): Sobala, L.F., Speciale, G., Hakki, Z., Fernandes, P.Z., Raich, L., Rojas-Cervellera, V., Bennet, A., Thompson, A.J., Bernardo-Seisdedos, G., Millet, O., Zhu, S., Lu, D., Sollogoub, M., Rovira, C., Jimenez-Barbero, J., Davies, G.J., Williams, S.J.
Funding Organization(s): European Research Council, Australian Research Council, Spanish Ministry of Economy and Competitiveness, Agency for Administration of University and Research, Generalitat de Catalunya

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.146
R-Value Work: 0.126
R-Value Observed: 0.127

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 44.39 kDa
Atom Count: 3,611
Modelled Residue Count: 349
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A	385	Bacteroides xylanisolvens XB1A	Mutation(s): 1 Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7 Go to UniProtKB: D6D1V7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6D1V7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
BO0 Query on BO0 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(1~{S},2~{S},3~{R},4~{R},6~{R})-4-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3-diol C₇ H₁₂ O₄ CQDNTUVVKVNNOI-BNWJMWRWSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.146
R-Value Work: 0.126
R-Value Observed: 0.127
Space Group: I 4
Diffraction Data: https://doi.org/10.5281/zenodo.4424526

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.233	α = 90
b = 108.233	β = 90
c = 67.446	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Bernardo-Seisdedos, G.

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Australian Research Council	Australia	FT130100103
Australian Research Council	Australia	DP120101396
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2017-85496-P
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-64597-C2-1P
Agency for Administration of University and Research	Spain	2017SGR-1189
Generalitat de Catalunya	Spain	2014SGR-987

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2020-06-10
Changes: Data collection, Database references
Version 1.2: 2020-07-08
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2021-02-03
Changes: Data collection, Database references, Structure summary
Version 1.5: 2024-01-17
Changes: Data collection, Database references, Refinement description