4QJI | pdb_00004qji

Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb4QJI/pdb

• Classification: LIGASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-03 Released: 2014-07-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis

Dranow, D.M., Abendroth, J., Wernimont, A.K., Edwards, T.E., Lorimer, D.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.56 kDa 
• Atom Count: 3,090 
• Modeled Residue Count: 428 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantothenate--cysteine ligase	A, B	237	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: coaBC, MSMEG_3054, MSMEI_2978 EC: 6.3.2.5 (PDB Primary Data), 4.1.1.36 (UniProt)
UniProt
Find proteins for A0QWT2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QWT2  Go to UniProtKB:  A0QWT2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP	C [auth A], E [auth B]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34QJI

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.58	α = 90
b = 90.58	β = 90
c = 109.57	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-09-19
  Changes: Data collection, Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description