5EG5 | pdb_00005eg5

As (III) S-adenosylmethyltransferase cysteine mutant C72A bound Phenylarsine oxide (PhAs(III) in the arsenic binding site

• PDB DOI: https://doi.org/10.2210/pdb5EG5/pdb

• Classification: TRANSFERASE
• Organism(s): Cyanidioschyzon sp. 5508
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-10-26 Released: 2016-11-02 
• Deposition Author(s): Packianathan, C., Marapakala, K., Kandavelu, P., Rosen, B.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

As (III) S-adenosylmethyltransferase cysteine mutant C72A bound Phenylarsine oxide (PhAs(III) in the arsenic binding site

Packianathan, C., Marapakala, K., Kandavelu, P., Rosen, B.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 41.98 kDa 
• Atom Count: 2,729 
• Modeled Residue Count: 322 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenic methyltransferase	A	377	Cyanidioschyzon sp. 5508	Mutation(s): 1  Gene Names: arsM EC: 2.1.1.137
UniProt
Find proteins for C0JV69 (Cyanidioschyzon sp. 5508) Explore C0JV69  Go to UniProtKB:  C0JV69

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PA0	B [auth A]	Phenylarsine oxide C6 H5 As O BQVCCPGCDUSGOE-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.255	α = 90
b = 47.369	β = 113.59
c = 100.261	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Packianathan, C., Marapakala, K., Kandavelu, P., Rosen, B.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R37GM55425

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description