4O7W | pdb_00004o7w

SAICAR synthetase (Type-2) in complex with ATP and TDP

• PDB DOI: https://doi.org/10.2210/pdb4O7W/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-26 Released: 2014-12-31 
• Deposition Author(s): Manjunath, K., Jeyakanthan, J., Sekar, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

SAICAR synthetase (Type-2) in complex with ATP and TDP

Manjunath, K., Jeyakanthan, J., Sekar, K.

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: 28.54 kDa 
• Atom Count: 2,014 
• Modeled Residue Count: 232 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A	238	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0239, purC EC: 6.3.2.6
UniProt
Find proteins for O57978 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57978  Go to UniProtKB:  O57978

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
TYD	B [auth A]	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.15	α = 90
b = 154.53	β = 90
c = 78.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Manjunath, K., Jeyakanthan, J., Sekar, K.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description