5DRH | pdb_00005drh

Crystal structure of apo C-As lyase

• PDB DOI: https://doi.org/10.2210/pdb5DRH/pdb

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


• Deposited: 2015-09-15 Released: 2016-09-21 
• 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: 2.27 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of apo C-As lyase

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 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.48 kDa 
• Atom Count: 850 
• Modeled Residue Count: 110 
• 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): 0  Gene Names: Tcur_4156 EC: 4 (PDB Primary Data), 1.13.11 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.12	α = 90
b = 44.12	β = 90
c = 117.56	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: 2016-09-21 
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 GM55425

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-09-13
  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, Refinement description