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- PDB-9gpi: Structure of RmlD from Trichomonas vaginalis is space group P1 -

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Basic information

Entry
Database: PDB / ID: 9gpi
TitleStructure of RmlD from Trichomonas vaginalis is space group P1
ComponentsdTDP-4-dehydrorhamnose reductase, putative
KeywordsCYTOSOLIC PROTEIN / Rhamnose / reductase / parasite
Function / homologyRmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding domain superfamily / dTDP-4-dehydrorhamnose reductase, putative
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGabrielsen, M. / Liu, Y.-C. / Kamarainen, O. / Acosta-Serrano, A. / Mottram, J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust80400 United Kingdom
CitationJournal: Wellcome Open Res / Year: 2025
Title: Structural analysis of RmlD, a dTDP-6-deoxy-L-lyxo-4-hexulose reductase from Trichomonas vaginalis
Authors: Gabrielsen, M. / Liu, Y.-C. / Kamarainen, O. / Acosta-Serrano, A. / Mottram, J.C.
History
DepositionSep 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: dTDP-4-dehydrorhamnose reductase, putative
B: dTDP-4-dehydrorhamnose reductase, putative
C: dTDP-4-dehydrorhamnose reductase, putative
A: dTDP-4-dehydrorhamnose reductase, putative


Theoretical massNumber of molelcules
Total (without water)128,1814
Polymers128,1814
Non-polymers00
Water1,24369
1
D: dTDP-4-dehydrorhamnose reductase, putative
B: dTDP-4-dehydrorhamnose reductase, putative


Theoretical massNumber of molelcules
Total (without water)64,0912
Polymers64,0912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-11 kcal/mol
Surface area25020 Å2
MethodPISA
2
C: dTDP-4-dehydrorhamnose reductase, putative
A: dTDP-4-dehydrorhamnose reductase, putative


Theoretical massNumber of molelcules
Total (without water)64,0912
Polymers64,0912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-11 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.085, 66.981, 85.822
Angle α, β, γ (deg.)91.160, 100.656, 116.151
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
dTDP-4-dehydrorhamnose reductase, putative


Mass: 32045.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_357160 / Production host: Escherichia coli (E. coli) / References: UniProt: A2FWC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM magnesium formate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9722 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9722 Å / Relative weight: 1
ReflectionResolution: 2.4→52.08 Å / Num. obs: 69087 / % possible obs: 88.23 % / Redundancy: 5.6 % / Biso Wilson estimate: 40.51 Å2 / CC1/2: 0.695 / CC star: 0.906 / Rmerge(I) obs: 0.6308 / Rpim(I) all: 0.2915 / Net I/σ(I): 1.2
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.441 / Num. unique obs: 3179 / CC1/2: 0.453 / Rpim(I) all: 0.6662 / % possible all: 71.69

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→52.02 Å / SU ML: 0.4112 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.5509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2934 3524 5.1 %
Rwork0.2384 65563 -
obs0.2412 69087 77.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→52.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8851 0 0 69 8920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00499020
X-RAY DIFFRACTIONf_angle_d0.863412224
X-RAY DIFFRACTIONf_chiral_restr0.05231406
X-RAY DIFFRACTIONf_plane_restr0.00531577
X-RAY DIFFRACTIONf_dihedral_angle_d5.96231209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.36751050.31791862X-RAY DIFFRACTION55.98
2.43-2.470.30551210.31482078X-RAY DIFFRACTION60.71
2.47-2.50.41431290.32692337X-RAY DIFFRACTION69.58
2.5-2.540.44411430.31192638X-RAY DIFFRACTION79.05
2.54-2.590.39371450.32082734X-RAY DIFFRACTION81.7
2.59-2.630.37321250.31282728X-RAY DIFFRACTION79.83
2.63-2.680.40721470.30442806X-RAY DIFFRACTION82.35
2.68-2.730.33581180.30042677X-RAY DIFFRACTION80.41
2.73-2.780.37691740.29682793X-RAY DIFFRACTION82.19
2.79-2.850.36961490.2952693X-RAY DIFFRACTION81.67
2.85-2.910.33041410.29222798X-RAY DIFFRACTION81.1
2.91-2.980.39311360.27952670X-RAY DIFFRACTION81.24
2.98-3.070.39591220.27322766X-RAY DIFFRACTION80.54
3.07-3.160.33341580.27512799X-RAY DIFFRACTION83.25
3.16-3.260.28791310.26142707X-RAY DIFFRACTION80.08
3.26-3.370.32191790.25842740X-RAY DIFFRACTION82.41
3.37-3.510.30081290.25682766X-RAY DIFFRACTION81.73
3.51-3.670.35251350.28442465X-RAY DIFFRACTION72.71
3.67-3.860.38181070.27362487X-RAY DIFFRACTION73.69
3.86-4.10.2981440.21132674X-RAY DIFFRACTION79.47
4.1-4.420.24371480.19482696X-RAY DIFFRACTION80.16
4.42-4.860.1951700.17112663X-RAY DIFFRACTION79.89
4.87-5.570.21711340.17662700X-RAY DIFFRACTION79.52
5.57-7.010.21391760.19172317X-RAY DIFFRACTION70.94
7.02-52.020.18791580.15782969X-RAY DIFFRACTION88.03
Refinement TLS params.Method: refined / Origin x: -11.4487198875 Å / Origin y: 16.4740601872 Å / Origin z: 23.2328489759 Å
111213212223313233
T0.219009288262 Å2-0.0126038739023 Å2-0.048901297213 Å2-0.308647968549 Å2-0.00502816397828 Å2--0.287209249542 Å2
L0.0566563250298 °2-0.0865750618732 °2-0.147667027243 °2-0.523793088209 °2-0.0320390917347 °2--0.451662069322 °2
S0.0151773422448 Å °-0.0478980318838 Å °0.0151184930559 Å °0.0083451381276 Å °0.0272028985463 Å °0.020086113024 Å °0.0144085889795 Å °0.0823675179059 Å °-0.0409344188628 Å °
Refinement TLS groupSelection details: all

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