3GTD | pdb_00003gtd

2.4 Angstrom crystal structure of fumarate hydratase from Rickettsia prowazekii

• PDB DOI: https://doi.org/10.2210/pdb3GTD/pdb

• Classification: LYASE
• Organism(s): Rickettsia prowazekii str. Madrid E
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-27 Released: 2009-07-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structure of fumarate hydratase from Rickettsia prowazekii, the agent of typhus and suspected relative of the mitochondria.

Phan, I., Subramanian, S., Olsen, C., Edwards, T.E., Guo, W., Zhang, Y., Van Voorhis, W.C., Stewart, L.J., Myler, P.J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1123-1128

• PubMed: 21904061 
• DOI: https://doi.org/10.1107/S174430911102690X
• Primary Citation Related Structures: 
  3GTD


• PubMed Abstract: 
  

  Rickettsiae are obligate intracellular parasites of eukaryotic cells that are the causative agents responsible for spotted fever and typhus. Their small genome (about 800 protein-coding genes) is highly conserved across species and has been postulated as the ancestor of the mitochondria. No genes that are required for glycolysis are found in the Rickettsia prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in both. A 2.4 Å resolution crystal structure of R. prowazekii fumarate hydratase, an enzyme catalyzing the third step of the tricarboxylic acid cycle pathway that ultimately converts phosphoenolpyruvate into succinyl-CoA, has been solved. A structure alignment with human mitochondrial fumarate hydratase highlights the close similarity between R. prowazekii and mitochondrial enzymes.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Diseases (SSGCID), USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 106.94 kDa 
• Atom Count: 6,784 
• Modeled Residue Count: 855 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase class II	A, B	482	Rickettsia prowazekii str. Madrid E	Mutation(s): 0  Gene Names: fumC, RP665 EC: 4.2.1.2
UniProt
Find proteins for Q9ZCQ4 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZCQ4  Go to UniProtKB:  Q9ZCQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], E [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GTD

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.9	α = 90
b = 144.9	β = 90
c = 106.21	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description