9GPI | pdb_00009gpi

Structure of RmlD from Trichomonas vaginalis is space group P1

• PDB DOI: https://doi.org/10.2210/pdb9GPI/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Trichomonas vaginalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-07 Released: 2025-03-12 
• Deposition Author(s): Gabrielsen, M., Liu, Y.-C., Kamarainen, O., Acosta-Serrano, A., Mottram, J.C.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of RmlD, a dTDP-6-deoxy-L-lyxo-4-hexulose reductase from Trichomonas vaginalis

Gabrielsen, M., Liu, Y.-C., Kamarainen, O., Acosta-Serrano, A., Mottram, J.C.

(2025) Wellcome Open Res 

• DOI: https://doi.org/10.12688/wellcomeopenres.23630.1

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.18 kDa 
• Atom Count: 8,920 
• Modeled Residue Count: 1,137 
• Deposited Residue Count: 1,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose reductase, putative	A [auth D], B, C, D [auth A]	286	Trichomonas vaginalis	Mutation(s): 0  Gene Names: TVAG_357160
UniProt
Find proteins for A2FWC8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2FWC8  Go to UniProtKB:  A2FWC8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.085	α = 91.16
b = 66.981	β = 100.656
c = 85.822	γ = 116.151

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Gabrielsen, M., Liu, Y.-C., Kamarainen, O., Acosta-Serrano, A., Mottram, J.C.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	80400

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-10-01
  Changes: Database references