6FXS | pdb_00006fxs

Structure of Trypanosoma brucei type B ribose 5-phosphate isomerase

• PDB DOI: https://doi.org/10.2210/pdb6FXS/pdb

• Classification: ISOMERASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-09 Released: 2019-05-22 
• Deposition Author(s): Ronin, C., Ciesielski, F., Ciapetti, P.
• Funding Organization(s): European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structure of Trypanosoma brucei type B ribose 5-phosphate isomerase (TbRpiB)

Ronin, C., Ciesielski, F., Ciapetti, P.

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)

Macromolecule Content 

• Total Structure Weight: 38.62 kDa 
• Atom Count: 2,459 
• Modeled Residue Count: 298 
• Deposited Residue Count: 350 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase, putative	A	175	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb11.01.0700 EC: 5.3.1.6
UniProt
Find proteins for Q384D1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q384D1  Go to UniProtKB:  Q384D1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase, putative	B	175	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb11.01.0700 EC: 5.3.1.6
UniProt
Find proteins for Q384D1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q384D1  Go to UniProtKB:  Q384D1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.8	α = 90
b = 97.8	β = 90
c = 84.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Ronin, C., Ciesielski, F., Ciapetti, P.

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Funding Organization	Location	Grant Number
European Communitys Seventh Framework Programme	France	602773

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-17
  Changes: Author supporting evidence, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary