5MQP

Glycoside hydrolase BT_1002

• PDB DOI: https://doi.org/10.2210/pdb5MQP/pdb

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


• Deposited: 2016-12-20 Released: 2017-04-05 
• Deposition Author(s): Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.
• Funding Organization(s): iotechnology and Biological Research Council, Biotechnology and Biological Sciences Research Council, Wellcome Trust, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Models: experimental

Literature

The most complex carbohydrate known is degraded in the human gut by single organisms and not bacterial consortia

Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Basle, A., Gray, J., Venditto, I., Briggs, B., Zhang, X., Labourel, A., Terrapon, N., Buffetto, F., Nepogodiev, S., Xiao, Y., Field, R.A., Zhu, Y., ONeil, M.A., Urbanowicz, B.R., York, W.S., Davies, G.J., Abbott, D.W., Ralet, M.-C., Martens, E.C., Henrissat, B., Gilbert, H.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 565.92 kDa 
• Atom Count: 41,129 
• Modelled Residue Count: 4,801 
• Deposited Residue Count: 4,992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase BT_1002	A, B, C, D, E, F, G, H	624	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: Btheta7330_02618
UniProt
Find proteins for Q8A915 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A915  Go to UniProtKB:  Q8A915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth E], O [auth E], P [auth F], Q [auth G], R [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.23	α = 90
b = 133.238	β = 97.67
c = 224.077	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
Coot	model building
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.

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Funding Organization	Location	Grant Number
iotechnology and Biological Research Council	United Kingdom	BB/K020358/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K001949/1
Wellcome Trust	United Kingdom	WT097907MA
European Research Council	United Kingdom	322820

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Author supporting evidence
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description