5V0F | pdb_00005v0f

Crystal structure of C-As lyase with mutation K105A and substrate Roxarsone

• PDB DOI: https://doi.org/10.2210/pdb5V0F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermomonospora curvata DSM 43183
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-28 Released: 2018-03-21 
• Deposition Author(s): Venkadesh, S., Yoshinaga, M., Sankaran, B., 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: 2.23 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of C-As lyase with mutation K105A and substrate Roxarsone.

Venkadesh, S., Yoshinaga, M., Sankaran, B., 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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.7 kDa 
• Atom Count: 916 
• Modeled Residue Count: 119 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A	126	Thermomonospora curvata DSM 43183	Mutation(s): 1  Gene Names: Tcur_4156 EC: 1.13.11
UniProt
Find proteins for D1A230 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A230  Go to UniProtKB:  D1A230

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RXO	B [auth A]	4-arsanyl-2-nitrophenol C6 H6 As N O3 POYWCBSQXBGKKH-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.73	α = 90
b = 41.73	β = 90
c = 119.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Venkadesh, S., Yoshinaga, M., Sankaran, B., 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	R37 GM055425

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description