7JKR | pdb_00007jkr

GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, phosphohistidine loop pointing towards nucleotide binding site

• PDB DOI: https://doi.org/10.2210/pdb7JKR/pdb

• Classification: LIGASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-28 Released: 2021-03-10 
• Deposition Author(s): Huang, J., Fraser, M.E.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase

Huang, J., Fraser, M.E.

(2021) Acta Crystallogr D Biol Crystallogr 77: 357-368

• DOI: https://doi.org/10.1107/S2059798321000334

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.44 kDa 
• Atom Count: 5,231 
• Modeled Residue Count: 692 
• Deposited Residue Count: 700 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	A	305	Sus scrofa	Mutation(s): 0  Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
UniProt
Find proteins for O19069 (Sus scrofa) Explore O19069  Go to UniProtKB:  O19069

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial	B	395	Sus scrofa	Mutation(s): 0  Gene Names: SUCLG2 EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa) Explore P53590  Go to UniProtKB:  P53590

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.328	α = 90
b = 99.328	β = 90
c = 134.029	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Huang, J., Fraser, M.E.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	04815-2019

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary