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- PDB-10gi: Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Babesi... -

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Basic information

Entry
Database: PDB / ID: 10gi
TitleStructure of Glyceraldehyde-3-Phosphate Dehydrogenase from Babesia bovis
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Bovine babesiosis / Babesia bovis / GAPDH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBabesia bovis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsUkrainski, B. / Galvao, E.B. / Silva, M. / Iulek, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other governmentPBA2025201000175 Brazil
CitationJournal: Protein Expr.Purif. / Year: 2026
Title: Expression, purification, crystallization and structure solution of glyceraldehyde-3-phosphate dehydrogenase from the babesiosis infective agent Babesia bovis.
Authors: Ukrainski, B. / Galvao, E.B. / Silva, M. / Iulek, J.
History
DepositionJan 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3344
Polymers77,0082
Non-polymers1,3272
Water50428
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,6698
Polymers154,0154
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555y,x,-z1
Buried area19720 Å2
ΔGint-125 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.614, 85.614, 155.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38503.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion with a His-tag / Source: (gene. exp.) Babesia bovis (eukaryote) / Gene: BBOV_II002540 / Production host: Escherichia coli (E. coli) / Strain (production host): E coli Rosetta(DE3)pLysS
References: UniProt: A7ATE8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 42.26 % / Description: Clustered plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 mol/L TRIS pH 8.5, 25% (m/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2025
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 3.118→74.201 Å / Num. obs: 9849 / % possible obs: 90.9 % / Redundancy: 19 % / Biso Wilson estimate: 111.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.394 / Rpim(I) all: 0.094 / Rrim(I) all: 0.405 / Net I/σ(I): 7.2
Reflection shellResolution: 3.118→3.512 Å / Redundancy: 19.9 % / Rmerge(I) obs: 3.951 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1414 / CC1/2: 0.486 / Rpim(I) all: 0.9 / Rrim(I) all: 4.054 / % possible all: 63.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALS3.14.2data reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→74.14 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / Phase error: 41.87
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Statistics output with a spherical consideration for resolution ranges, while data were processed anisotropically.
RfactorNum. reflection% reflectionSelection details
Rfree0.3405 513 5.22 %Random, respect possible twin
Rwork0.2897 9324 --
obs0.2926 9837 80.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.2 Å2
Refinement stepCycle: LAST / Resolution: 3.12→74.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 88 28 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00145152
X-RAY DIFFRACTIONf_angle_d0.38497030
X-RAY DIFFRACTIONf_chiral_restr0.0417812
X-RAY DIFFRACTIONf_plane_restr0.0027900
X-RAY DIFFRACTIONf_dihedral_angle_d9.8631858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.430.3923350.3818967X-RAY DIFFRACTION33.5
3.43-3.930.40871470.37112460X-RAY DIFFRACTION86.78
3.93-4.950.35181740.32692862X-RAY DIFFRACTION99.8
4.95-74.140.30681570.23653035X-RAY DIFFRACTION99.87
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)
11.05629316086-0.432563973244-1.416495582331.101108512111.467450538512.67160001428-0.02203036232780.0247100747774-0.27788163561-0.1140028636170.249264166451-0.5373336263730.6437194674241.12011286885-0.1535763566991.15764399175-0.04041590426590.1161730989051.32665930317-0.2253395423310.63945041043237.23869365065.22531661239-6.91800577884
20.71913126403-0.638324341853-0.3903335539480.9040596023130.6293645538460.44999709457-0.280187759839-0.0298793369803-0.3953370346010.2792773257820.05434345534570.02714661967780.4126501622120.3418154072640.157420264751.859304671740.06671809038940.3167939109190.767101714675-0.1583357768830.69728025456126.4276779003-10.301902729-10.7830829263
31.17686462993-0.221871531036-0.2362929796241.49474204129-0.2275136396080.410872297411-0.339147108734-0.220442541482-1.077415709110.631374992432-0.1283724869690.457555920541.29810713621-0.06731196040210.3072809165182.02408234509-1.255764774520.484766038137-0.771544057813-0.1334050706340.6744141475329.92927915264-1.29015237655-0.105857118298
40.0795685609666-0.1542352631440.04135482475921.69927611473-0.8947561526810.434753399711-0.179384068041-0.0237747993326-0.48215557062-0.5671045869170.1733946237430.4237600524710.5547757369980.3411768997710.03633867689161.82170053993-0.710761474830.5769456880490.1409400321030.04420591344051.0060626495417.3998718969-2.544363437185.09459598831
51.16080481410.932067337080.1061885057221.02123013817-0.9331577536543.60150020267-0.08905223361341.034973916950.463149303103-0.622256699006-0.1388775474640.0716999324527-0.552247687852-0.7367740832280.117538693211.535683785530.3781909513680.5668925290081.319153444420.4022754705150.6266965667267.7419962666529.9419050404-29.1628442825
62.98311986483-0.109415911785-4.659972806260.9066317942841.213994080638.3729255055-0.2105587095122.156749983590.2166945274-0.786345145138-0.377190872370.0372424296126-0.189548334165-0.8631302803150.4180219155381.355507907670.0236141085350.09449819920671.563416216050.1967996547110.5552559035995.8219002968721.5829692747-29.0721075575
70.316722996986-0.01584578139580.2275605592580.000374486416054-0.02098478697880.176736078547-0.1160174346630.7200613369720.335136918589-0.385149429362-0.0941672157937-0.151022160015-0.4619666472710.2184893863480.1792278772751.52478074561-0.286067120440.8817614328551.732788666190.6137946262051.3060253442921.087710057234.0152507402-32.1773809177
80.5433743036060.1769914758760.1235276847350.769072078788-0.08126586804590.0501815205885-0.04111467432110.6755788118010.276905250353-0.275205141418-0.0923346047394-0.176757139166-0.3227400111570.354955756930.1267658664731.86027880695-0.6407102149840.8082849671041.081396242310.7456727098331.5812595321118.672147078347.5500102899-22.1636670533
91.62003792338-0.6661864811110.6258192543910.295121147851-0.3025014033940.5328516041740.04343083972360.4582059287280.924227193099-0.2362825707120.210461431848-0.434683103695-0.3708816072320.500238357439-0.1288963485481.30495544016-0.8383145733510.4613314149510.47328734855-0.1203831572530.86355991483324.775715897829.2243737071-7.99892537967
100.0002468210904710.0706162388155-0.02741832156460.420826325127-0.1528258555220.06173580805630.004496815421140.4017024460850.890058095946-0.1147778775190.0822300502339-0.275758018341-0.6566218448540.1845126975250.1299424741351.79218807537-0.6853859845570.444527380950.5343341609010.1122374852621.7165286862120.723561700946.2116688726-7.89982052282
110.035740287076-0.1073501620160.02319260751750.305700606461-0.07513298040250.016758946005-0.1039521468280.3666903146390.872574246368-0.144757676594-0.0962319372136-0.112373105712-0.714637425270.2843851004350.1979214250341.81010620363-0.3647218317930.5782878445940.4232721575380.4435149531021.523988857166.4388409819643.9251955018-8.64601385557
120.647862023740.0616395564184-0.1622790282070.898871309844-0.2972582067670.130049280531-0.1988813878370.5066939604310.756116622031-0.164823083794-0.203053092591-0.108253040382-0.5947360902180.1963864042980.2025754132771.89537730884-0.4592602048650.4039844314570.5810291906740.6748663699581.6093401734813.896232972944.406403226-13.7577082704
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 103 )AA1 - 1031 - 103
22chain 'A' and (resid 104 through 153 )AA104 - 153104 - 153
33chain 'A' and (resid 154 through 284 )AA154 - 284154 - 284
44chain 'A' and (resid 285 through 337 )AA285 - 337285 - 337
55chain 'B' and (resid 0 through 38 )BC0 - 381 - 39
66chain 'B' and (resid 39 through 86 )BC39 - 8640 - 87
77chain 'B' and (resid 87 through 132 )BC87 - 13288 - 133
88chain 'B' and (resid 133 through 167 )BC133 - 167134 - 168
99chain 'B' and (resid 168 through 208 )BC168 - 208169 - 209
1010chain 'B' and (resid 209 through 269 )BC209 - 269210 - 270
1111chain 'B' and (resid 270 through 298 )BC270 - 298271 - 299
1212chain 'B' and (resid 299 through 337 )BC299 - 337300 - 338

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