5CB9 | pdb_00005cb9

Crystal structure of C-As lyase with mercaptoethonal

• PDB DOI: https://doi.org/10.2210/pdb5CB9/pdb

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


• Deposited: 2015-06-30 Released: 2016-07-13 
• 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: 1.95 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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: 13.63 kDa 
• Atom Count: 1,005 
• Modeled Residue Count: 118 
• 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: 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
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.66	α = 90
b = 42.66	β = 90
c = 116.96	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: 2016-07-13 
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: 2016-07-13
  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, Refinement description
• Version 1.4: 2024-05-01
  Changes: Derived calculations