2III

Crystal structure of the adenosylmethionine decarboxylase (aq_254) from aquifex aeolicus vf5

• PDB DOI: https://doi.org/10.2210/pdb2III/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-28 Released: 2007-10-09 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the adenosylmethionine decarboxylase (aq_254) from aquifex aeolicus vf5

Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 15.38 kDa 
• Atom Count: 1,041 
• Modelled Residue Count: 120 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine decarboxylase proenzyme	A	135	Aquifex aeolicus VF5	Mutation(s): 2  EC: 4.1.1.50
UniProt
Find proteins for O66615 (Aquifex aeolicus (strain VF5)) Explore O66615  Go to UniProtKB:  O66615

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.30 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.792	α = 90
b = 41.792	β = 90
c = 134.921	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary