2PCN

Crystal structure of S-adenosylmethionine: 2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426

• PDB DOI: https://doi.org/10.2210/pdb2PCN/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-30 Released: 2007-10-02 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S-adenosylmethionine:2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426

Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.14 kDa 
• Atom Count: 1,455 
• Modelled Residue Count: 161 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine:2-demethylmenaquinone methyltransferase	A	161	Geobacillus kaustophilus HTA426	Mutation(s): 0  EC: 2.1.1 (PDB Primary Data), 4.1.3.17 (UniProt), 4.1.1.112 (UniProt)
UniProt
Find proteins for Q5KYY8 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KYY8  Go to UniProtKB:  Q5KYY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.573	α = 90
b = 84.573	β = 90
c = 83.338	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description