6GOC | pdb_00006goc

Methylesterase BT1017

• PDB DOI: https://doi.org/10.2210/pdb6GOC/pdb

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


• Deposited: 2018-06-01 Released: 2019-06-19 
• Deposition Author(s): Basle, A., Ndeh, D., Gilbert, H.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.211 (DCC) 

Literature

Characterisation of a methylesterases essential for pectin rhamnogalacturonan II metabolism from the gut bacterium Bacteroides thetaiotaomicron

Ndhe, D., Cheng-Jie, D., Basle, A., Gilbert, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.16 kDa 
• Atom Count: 3,753 
• Modeled Residue Count: 444 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3826 domain-containing protein	A	658	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: BJP75_005780, Btheta7330_02632
UniProt
Find proteins for Q8A900 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A900  Go to UniProtKB:  Q8A900

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.243 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.211 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.508	α = 90
b = 229.469	β = 90
c = 80.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
GDA	data collection
MOSFLM	data reduction
Aimless	data scaling
SHELXCD	phasing
SHELXE	model building
BUCCANEER	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Basle, A., Ndeh, D., Gilbert, H.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	322820

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 2.0: 2020-04-22
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary