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- PDB-8r3q: Transketolase from Plasmodium falciparum in complex with thiamin ... -

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Basic information

Entry
Database: PDB / ID: 8r3q
TitleTransketolase from Plasmodium falciparum in complex with thiamin pyrophosphate
Componentstransketolase
KeywordsCYTOSOLIC PROTEIN / transketolase / pentose phosphate pathway / infectious organism
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / nucleus / cytosol / cytoplasm
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
CITRIC ACID / THIAMINE DIPHOSPHATE / transketolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBallut, L. / Georges, R.N. / Aghajari, N. / Hecquet, L. / Charmantray, F. / Doumeche, B.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Biochemistry / Year: 2024
Title: Biochemical, Bioinformatic, and Structural Comparisons of Transketolases and Position of Human Transketolase in the Enzyme Evolution.
Authors: Georges, R.N. / Ballut, L. / Aghajari, N. / Hecquet, L. / Charmantray, F. / Doumeche, B.
History
DepositionNov 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: transketolase
A: transketolase
C: transketolase
D: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,21021
Polymers311,3324
Non-polymers2,87717
Water52,7662929
1
B: transketolase
A: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,13611
Polymers155,6662
Non-polymers1,4709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-55 kcal/mol
Surface area43020 Å2
2
C: transketolase
D: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,07410
Polymers155,6662
Non-polymers1,4088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-59 kcal/mol
Surface area43800 Å2
Unit cell
Length a, b, c (Å)97.040, 114.340, 149.900
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
transketolase


Mass: 77833.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_0610800 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KSV3

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Non-polymers , 5 types, 2946 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2929 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Li2SO4, 0.1 M Sodium citrate pH 5.6, 12 % (w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.88→46.81 Å / Num. obs: 265236 / % possible obs: 99.95 % / Redundancy: 6.93 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.84
Reflection shellResolution: 1.88→1.9 Å / Num. unique obs: 8293 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→46.81 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.9371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1679 13262 5 %
Rwork0.1442 251970 -
obs0.1454 265232 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.45 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21416 0 180 2929 24525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007522377
X-RAY DIFFRACTIONf_angle_d0.930346
X-RAY DIFFRACTIONf_chiral_restr0.06113222
X-RAY DIFFRACTIONf_plane_restr0.00793974
X-RAY DIFFRACTIONf_dihedral_angle_d8.84462989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.3054430.26818412X-RAY DIFFRACTION99.89
1.9-1.920.26594380.22818339X-RAY DIFFRACTION99.92
1.92-1.950.25744430.2078411X-RAY DIFFRACTION99.97
1.95-1.970.22784410.18978371X-RAY DIFFRACTION99.98
1.97-20.20044360.17178313X-RAY DIFFRACTION99.93
2-2.030.21044430.16098413X-RAY DIFFRACTION99.99
2.03-2.050.20294400.16038364X-RAY DIFFRACTION100
2.05-2.080.18494400.15418359X-RAY DIFFRACTION99.99
2.08-2.120.18134430.14878421X-RAY DIFFRACTION99.99
2.12-2.150.17974390.15078334X-RAY DIFFRACTION99.99
2.15-2.190.17784400.15198348X-RAY DIFFRACTION99.99
2.19-2.230.1864410.1468387X-RAY DIFFRACTION99.98
2.23-2.270.18224430.14878416X-RAY DIFFRACTION100
2.27-2.320.1814400.14848350X-RAY DIFFRACTION99.97
2.32-2.370.18014400.15078372X-RAY DIFFRACTION99.97
2.37-2.420.16624430.14778416X-RAY DIFFRACTION99.98
2.42-2.480.17694430.1438403X-RAY DIFFRACTION99.95
2.48-2.550.16634410.14128382X-RAY DIFFRACTION99.94
2.55-2.630.16454410.13788389X-RAY DIFFRACTION100
2.63-2.710.17464410.14048376X-RAY DIFFRACTION99.99
2.71-2.810.17844400.14298355X-RAY DIFFRACTION99.99
2.81-2.920.16244440.14078428X-RAY DIFFRACTION99.98
2.92-3.050.1644420.14128401X-RAY DIFFRACTION100
3.05-3.210.15744430.13738427X-RAY DIFFRACTION99.98
3.21-3.420.1454450.13718443X-RAY DIFFRACTION99.91
3.42-3.680.13544420.12718398X-RAY DIFFRACTION99.92
3.68-4.050.13574440.11828440X-RAY DIFFRACTION99.84
4.05-4.630.11864440.11418441X-RAY DIFFRACTION99.97
4.64-5.840.15614460.13698463X-RAY DIFFRACTION99.93
5.84-46.810.17574530.15118598X-RAY DIFFRACTION99.58

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