1K3R

Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum

• PDB DOI: https://doi.org/10.2210/pdb1K3R/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-10-03 Released: 2002-05-15 
• Deposition Author(s): Zarembinski, T.I., Kim, Y., Peterson, K., Christendat, D., Dharamsi, A., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.221 
• R-Value Observed: 0.227 

Literature

Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.

Zarembinski, T.I., Kim, Y., Peterson, K., Christendat, D., Dharamsi, A., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A.

(2003) Proteins 50: 177-183

• PubMed: 12486711 
• DOI: https://doi.org/10.1002/prot.10311
• Primary Citation of Related Structures:  
  1K3R

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Organizational Affiliation: 

Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 60.47 kDa 
• Atom Count: 4,278 
• Modelled Residue Count: 526 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved protein MT0001	A, B	268	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O26109 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26109  Go to UniProtKB:  O26109

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.221 
• R-Value Observed: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.307	α = 90
b = 51.353	β = 94.69
c = 109.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-15 
Deposition Author(s): Zarembinski, T.I., Kim, Y., Peterson, K., Christendat, D., Dharamsi, A., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2002-05-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references