3DLI | pdb_00003dli

Crystal structure of a SAM dependent methyltransferase from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb3DLI/pdb

• Classification: TRANSFERASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-27 Released: 2008-07-15 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystal structure of a SAM dependent methyltransferase from Archaeoglobus fulgidus

Agarwal, R., Burley, S.K., Swaminathan, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.47 kDa 
• Atom Count: 5,647 
• Modeled Residue Count: 663 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methyltransferase	A, B, C	240	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: AF_0046
UniProt
Find proteins for O30190 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30190  Go to UniProtKB:  O30190

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.154	α = 90
b = 81.88	β = 90
c = 122.797	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references