3DH7 | pdb_00003dh7

Structure of T. thermophilus IDI-2 in complex with PPi

• PDB DOI: https://doi.org/10.2210/pdb3DH7/pdb

• Classification: ISOMERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-17 Released: 2008-09-23 
• Deposition Author(s): de Ruyck, J., Wouters, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate

de Ruyck, J., Pouyez, J., Rothman, S.C., Poulter, D., Wouters, J.

(2008) Biochemistry 47: 9051-9053

• PubMed: 18693754 
• DOI: https://doi.org/10.1021/bi801159x
• Primary Citation Related Structures: 
  3DH7


• PubMed Abstract: 
  

  The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase in complex with inorganic pyrophosphate, providing new insights about the active site and the catalytic mechanism of the enzyme. The PP i moiety is located near the conserved residues, H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site of isopentenyl diphosphate isomerase 2 provides interactions for stabilizing a carbocationic intermediate similar to those that stabilize the intermediate in the well-established protonation-deprotonation mechanism of isopentenyl diphosphate isomerase 1.

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Organizational Affiliation: 
• Department of Chemistry, University of Namur, Namur, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (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: 146.44 kDa 
• Atom Count: 9,991 
• Modeled Residue Count: 1,265 
• Deposited Residue Count: 1,328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopentenyl-diphosphate delta-isomerase	A, B, C, D	332	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHB110 EC: 5.3.3.2
UniProt
Find proteins for Q53W52 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W52  Go to UniProtKB:  Q53W52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], F [auth B], H [auth C], I [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
POP	G [auth B], J [auth D]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.528	α = 90
b = 142.528	β = 90
c = 109.682	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): de Ruyck, J., Wouters, J.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations