5D4F

Crystal structure of C-As lyase with Fe(III)

• PDB DOI: https://doi.org/10.2210/pdb5D4F/pdb

• Classification: LYASE
• Organism(s): Thermomonospora curvata DSM 43183
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-07 Released: 2016-09-07 
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.234 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Crystal structure of C-As lyase with mercaptoethonal

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.33 kDa 
• Atom Count: 884 
• Modelled Residue Count: 108 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A	123	Thermomonospora curvata DSM 43183	Mutation(s): 0  Gene Names: Tcur_4156
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
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.234 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.37	α = 90
b = 42.37	β = 90
c = 116.9	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: 2016-09-07 
Deposition Author(s): Venkadesh, S., Yoshinaga, M., Sankaran, B., Kandavelu, P., Rosen, B.P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R37 GM55425

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2017-09-06
  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