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- PDB-9gsc: Structure of RmlD from Trichomonas vaginalis is space group P212121 -

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Basic information

Entry
Database: PDB / ID: 9gsc
TitleStructure of RmlD from Trichomonas vaginalis is space group P212121
ComponentsdTDP-4-dehydrorhamnose reductase, putative
KeywordsCYTOSOLIC PROTEIN / Rhamnose / reductase / parasite
Function / homologyRmlD-like substrate binding domain / RmlD substrate binding domain / biosynthetic process / 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: 2.8 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: To Be Published
Title: Structure of RmlD from T. vaginalis in space group P212121
Authors: Gabrielsen, M. / Liu, Y.-C. / Kamarainen, O. / Acosta-Serrano, A. / Mottram, J.C.
History
DepositionSep 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,1814
Polymers128,1814
Non-polymers00
Water905
1
A: dTDP-4-dehydrorhamnose reductase, putative
B: dTDP-4-dehydrorhamnose reductase, putative


Theoretical massNumber of molelcules
Total (without water)64,0912
Polymers64,0912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: dTDP-4-dehydrorhamnose reductase, putative
D: dTDP-4-dehydrorhamnose reductase, putative


Theoretical massNumber of molelcules
Total (without water)64,0912
Polymers64,0912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.400, 108.311, 153.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 31 or resid 36...
d_2ens_1(chain "B" and (resid 1 through 31 or resid 36...
d_3ens_1(chain "C" and (resid 1 through 39 or (resid 40...
d_4ens_1(chain "D" and (resid 1 through 31 or resid 36...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETTHRTHRAA1 - 312 - 32
d_12ASPASPLYSLYSAA36 - 27937 - 280
d_21METMETTHRTHRBB1 - 312 - 32
d_22ASPASPALAALABB36 - 6037 - 61
d_23LEULEULYSLYSBB79 - 27980 - 280
d_31METMETALAALACC1 - 602 - 61
d_32LEULEULYSLYSCC79 - 27980 - 280
d_41METMETTHRTHRDD1 - 312 - 32
d_42ASPASPALAALADD36 - 6037 - 61
d_43LEULEULYSLYSDD79 - 27980 - 280

NCS oper:
IDCodeMatrixVector
1given(0.981248516597, 0.00785670927774, 0.192586657884), (0.0140442527661, -0.999427371544, -0.0307845411317), (0.192234512093, 0.0329120210223, -0.980796967385)8.17156509257, -27.567047041, -81.5718223553
2given(-0.987804987003, 0.033499982857, -0.152049527458), (-0.0618284437276, -0.980676527309, 0.185609246352), (-0.142893495996, 0.192746724832, 0.970788416118)13.0139128739, -16.4866940233, 8.5816835945
3given(-0.997852644745, 0.050250830659, 0.0420113483982), (0.0408857853119, 0.978972105894, -0.199854868443), (-0.0511708113634, -0.197708042069, -0.978924449672)21.3022338288, -8.83543431823, -74.4688148254

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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.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 00 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→41.35 Å / Num. obs: 29580 / % possible obs: 89.48 % / Redundancy: 13.7 % / Biso Wilson estimate: 54.55 Å2 / CC1/2: 0.866 / Rmerge(I) obs: 0.697 / Net I/σ(I): 27.87
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 2773 / CC1/2: 0.518

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.35 Å / SU ML: 0.4084 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3036 1332 5.03 %
Rwork0.2631 25159 -
obs0.2651 26491 89.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.41 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8598 0 0 5 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00868760
X-RAY DIFFRACTIONf_angle_d1.496711853
X-RAY DIFFRACTIONf_chiral_restr0.08171359
X-RAY DIFFRACTIONf_plane_restr0.0091520
X-RAY DIFFRACTIONf_dihedral_angle_d10.95441161
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.03051407626
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.11087465356
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.12325838825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.37391420.34472631X-RAY DIFFRACTION95.55
2.9-3.020.41871340.34222655X-RAY DIFFRACTION95.61
3.02-3.150.33641350.33042626X-RAY DIFFRACTION95.14
3.15-3.320.36621470.31172615X-RAY DIFFRACTION94.52
3.32-3.530.36011320.28712635X-RAY DIFFRACTION94.02
3.53-3.80.32571460.26672527X-RAY DIFFRACTION91.26
3.8-4.180.27771410.26352369X-RAY DIFFRACTION84.83
4.18-4.790.26091110.22272237X-RAY DIFFRACTION79
4.79-6.030.28291240.2332231X-RAY DIFFRACTION78.71
6.03-41.350.23251200.21732633X-RAY DIFFRACTION87.45
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92243337463-0.636663217822-0.3065301677234.466904178181.102905176872.24666445569-0.0481191782973-0.0680696814396-0.266006551532-0.05230608976730.08538618159040.09370546990410.1799027995950.0796331606944-0.009012098261750.222420845718-0.0138864406322-0.01372637422840.369121743629-0.03280677289470.21591921574223.4280398104-11.861795552-20.2257376896
21.91771540569-0.441611227231-0.2268222570953.591077595550.6006397685742.47911166084-0.076603002522-0.00235384288945-0.0398187569010.05662455184280.0739594540579-0.0714674454461-0.1805043137590.1019811635150.0129630547890.2095057129480.0162808350998-0.02360648830220.4628877790250.01031241534630.19475621905727.9816693805-13.8474092776-58.146497928
31.542529425370.400586752073-0.3065045092353.59717837021-1.032488249951.792818126680.02203195597220.1146838404920.2794763438630.01699764538050.0957288358736-0.542242862532-0.08489828446920.0387312571772-0.1217905293710.271306406367-0.007477846746270.02688875165440.436716891996-0.09501485507640.572254748244-5.25354918078-15.6856478347-54.4199635983
42.45501161483-0.261632969209-0.9123293306592.30844797406-0.07611047508633.7475494909-0.15986541448-0.261496138396-0.189639223361-0.05732294085340.0433380684307-0.205838138470.1742006872960.1039110615010.09618929381760.300550608751-0.012730402291-0.002503917131220.315539723282-0.07373456750710.589415324272-8.93894280154-9.56136154302-16.540684126
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 0:281)BB0 - 2811 - 282
22(chain A and resseq 1:280)AA1 - 2801 - 262
33(chain C and resseq 1:279)CC1 - 2791 - 275
44(chain D and resseq 0:280)DD0 - 2801 - 274

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