3ENJ | pdb_00003enj

Structure of Pig Heart Citrate Synthase at 1.78 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ENJ/pdb

• Classification: LYASE, TRANSFERASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2008-09-25 Released: 2009-02-03 
• Deposition Author(s): Larson, S.B., Day, J.S., Nguyen, C., Cudney, R., McPherson, A., Center for High-Throughput Structural Biology (CHTSB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of pig heart citrate synthase at 1.78 A resolution.

Larson, S.B., Day, J.S., Nguyen, C., Cudney, R., McPherson, A.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 430-434

• PubMed: 19407370 
• DOI: https://doi.org/10.1107/S1744309109008343
• Primary Citation Related Structures: 
  3ENJ


• PubMed Abstract: 
  

  Pig heart citrate synthase was crystallized from a small-molecule cocktail containing cystamine dihydrochloride, aspartame and benzamidine hydrochloride. The structure was refined to an R factor of 0.179 (R(free) = 0.222) using synchrotron data to a resolution of 1.78 A. The model includes the full-length protein, a chloride ion, a sulfate ion, 305 water molecules and an unexpected moiety attached through a disulfide linkage to Cys184, which was modeled as a half-cystamine molecule generated by disulfide exchange with the cystamine in the small-molecule cocktail.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, The University of California, Irvine, 92697-3900, USA.

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: 49.23 kDa 
• Atom Count: 3,848 
• Modeled Residue Count: 437 
• Deposited Residue Count: 437 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A	437	Sus scrofa	Mutation(s): 0  EC: 2.3.3.1
UniProt
Find proteins for P00889 (Sus scrofa) Explore P00889  Go to UniProtKB:  P00889

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	B [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.34	α = 90
b = 76.34	β = 90
c = 198.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Larson, S.B., Day, J.S., Nguyen, C., Cudney, R., McPherson, A., Center for High-Throughput Structural Biology (CHTSB)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary