7RGC | pdb_00007rgc

Crystal structure of triosephosphate isomerase from Candidatus Absconditabacteria (Sr1) bacterium

• PDB DOI: https://doi.org/10.2210/pdb7RGC/pdb

• Classification: ISOMERASE
• Organism(s): candidate division SR1 bacterium RAAC1_SR1_1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-15 Released: 2022-07-20 
• Deposition Author(s): Vickers, C.J., Compton, J., Fraga, D., Patrick, W.M.
• Funding Organization(s): Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Structure of Sr1TPI - Candidatus Absconditabacteria bacterium triosephoshate isomerase

Vickers, C.J., Fraga, D., Compton, J., Patrick, W.M.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.21 kDa 
• Atom Count: 3,694 
• Modeled Residue Count: 480 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	247	candidate division SR1 bacterium RAAC1_SR1_1	Mutation(s): 0  Gene Names: tpiA, P148_SR1C00001G0257 EC: 5.3.1.1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.797	α = 90
b = 151.797	β = 90
c = 118.439	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Vickers, C.J., Compton, J., Fraga, D., Patrick, W.M.

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Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary