6HMG
Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine)
- PDB DOI: https://doi.org/10.2210/pdb6HMG/pdb
- Classification: HYDROLASE
- Organism(s): Bacteroides xylanisolvens XB1A
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2018-09-12 Released: 2018-09-26 
- Funding Organization(s): European Research Council, Spanish Ministry of Economy and Competitiveness
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.27 Å
- R-Value Free: 0.154 
- R-Value Work: 0.132 
- R-Value Observed: 0.133 
This is version 2.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glycosyl hydrolase family 71 | 385 | Bacteroides xylanisolvens XB1A | Mutation(s): 0  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 AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GLC Query on GLC | D [auth A] | alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N | |||
GDQ (Subject of Investigation/LOI) Query on GDQ | C [auth A] | (1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol C7 H13 N O3 JACJTGDBUDQHPY-VOQCIKJUSA-N | |||
ACT Query on ACT | B [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.27 Å
- R-Value Free: 0.154 
- R-Value Work: 0.132 
- R-Value Observed: 0.133 
- Space Group: I 4
- Diffraction Data: https://doi.org/10.5281/zenodo.4431701
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 108.772 | α = 90 |
b = 108.772 | β = 90 |
c = 67.703 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-09-26  Deposition Author(s): Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.
Funding Organization | Location | Grant Number |
---|---|---|
European Research Council | United Kingdom | 322942 |
Spanish Ministry of Economy and Competitiveness | Spain | CTQ2017-85496-P |
Spanish Ministry of Economy and Competitiveness | Spain | CTQ2015-64597-C2-1P |
Revision History (Full details and data files)
- Version 1.0: 2018-09-26
Type: Initial release - Version 1.1: 2018-11-28
Changes: Data collection, Database references - Version 2.0: 2018-12-19
Changes: Atomic model, Data collection, Derived calculations - Version 2.1: 2019-04-24
Changes: Data collection, Database references - Version 2.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.3: 2021-02-10
Changes: Database references, Structure summary - Version 2.4: 2024-01-24
Changes: Data collection, Database references, Refinement description