3T0I | pdb_00003t0i

Crystal structure of complex of BT_2972 and AdoHcy, a methyltransferase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3T0I/pdb

• Classification: TRANSFERASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-20 Released: 2011-09-07 
• Deposition Author(s): Kumar, V., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of complex of BT_2972 and AdoHcy,a methyltransferase from Bacteroides thetaiotaomicron

Kumar, V., Sivaraman, 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.

Macromolecule Content 

• Total Structure Weight: 61.4 kDa 
• Atom Count: 4,175 
• Modeled Residue Count: 490 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	263	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: NP_811884.1
UniProt
Find proteins for Q8A3I2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I2  Go to UniProtKB:  Q8A3I2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.642	α = 90
b = 74.525	β = 90
c = 117.221	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Kumar, V., Sivaraman, J.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-09-28
  Changes: Refinement description
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description