3NUA | pdb_00003nua

Crystal Structure of Phosphoribosylaminoimidazole-Succinocarboxamide Synthase from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb3NUA/pdb

• Classification: LIGASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-07-06 Released: 2010-08-25 
• Deposition Author(s): Kim, Y., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.161 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Phosphoribosylaminoimidazole-Succinocarboxamide Synthase from Clostridium perfringens

Kim, Y., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.73 kDa 
• Atom Count: 5,030 
• Modeled Residue Count: 473 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A, B	238	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: CPF_0673, purC EC: 6.3.2.6
UniProt
Find proteins for Q0TTB4 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore Q0TTB4  Go to UniProtKB:  Q0TTB4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], G [auth B], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CIT	E [auth A], I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.161 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33nua

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.877	α = 90
b = 148.913	β = 90
c = 45.315	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
BALBES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Kim, Y., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description