9GSC | pdb_00009gsc

Structure of RmlD from Trichomonas vaginalis is space group P212121

PDB DOI: https://doi.org/10.2210/pdb9GSC/pdb

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

Deposited: 2024-09-14 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.304 (Depositor), 0.307 (DCC)
R-Value Work:
0.263 (Depositor), 0.266 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 128.18 kDa
Atom Count: 8,603
Modeled Residue Count: 1,093
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose reductase, putative	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2FWC8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.304 (Depositor), 0.307 (DCC)
R-Value Work: 0.263 (Depositor), 0.266 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.4	α = 90
b = 108.311	β = 90
c = 153.266	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
d*TREK	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Acosta-Serrano, A.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	80400

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.