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- PDB-8r3o: Transketolase from Haemophilus influenzae in complex with thiamin... -

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Basic information

Entry
Database: PDB / ID: 8r3o
TitleTransketolase from Haemophilus influenzae 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 / metal ion binding / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / 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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBallut, L. / Georges, R.N. / Aghajari, N. / Hecquet, L. / Charmantray, F. / Doumeche, B.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Are Transketolases relevant Targets fighting Human Pathogens? A comparative Biochemical, Bioinformatic and Structural Study
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)301,39917
Polymers298,9004
Non-polymers2,49913
Water41,6332311
1
A: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,6038
Polymers149,4502
Non-polymers1,1536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-51 kcal/mol
Surface area39750 Å2
2
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,7969
Polymers149,4502
Non-polymers1,3467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-51 kcal/mol
Surface area39650 Å2
Unit cell
Length a, b, c (Å)110.250, 90.670, 155.250
Angle α, β, γ (deg.)90.000, 100.950, 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 ABCD

#1: Protein
Transketolase


Mass: 74725.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: tktA / Production host: Escherichia coli (E. coli) / References: UniProt: P43757

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Non-polymers , 5 types, 2324 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2311 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium acetate, 0.1 M Sodium citrate pH 5.6, 8 % (w/v), PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9676 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9676 Å / Relative weight: 1
ReflectionResolution: 2.1→34.82 Å / Num. obs: 168690 / % possible obs: 96.3 % / Redundancy: 3.34 % / Biso Wilson estimate: 25.2 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.68
Reflection shellResolution: 2.1→2.9 Å / Num. unique obs: 104558 / CC1/2: 0.978

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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: 2.1→34.82 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.6883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1908 8435 5 %
Rwork0.1491 160255 -
obs0.1512 168690 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20532 0 155 2311 22998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006721174
X-RAY DIFFRACTIONf_angle_d0.802328716
X-RAY DIFFRACTIONf_chiral_restr0.04993052
X-RAY DIFFRACTIONf_plane_restr0.00823765
X-RAY DIFFRACTIONf_dihedral_angle_d8.24532914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.36682810.31465338X-RAY DIFFRACTION96.98
2.12-2.150.31562830.28075366X-RAY DIFFRACTION97.36
2.15-2.180.27732820.23685365X-RAY DIFFRACTION97.53
2.18-2.20.29192840.22245391X-RAY DIFFRACTION97.42
2.2-2.230.26052830.18965367X-RAY DIFFRACTION97.4
2.23-2.260.2392820.18365372X-RAY DIFFRACTION97.3
2.26-2.290.23512840.17625390X-RAY DIFFRACTION97.26
2.29-2.330.23882840.16995389X-RAY DIFFRACTION97.57
2.33-2.370.23282820.17145370X-RAY DIFFRACTION97.43
2.37-2.40.21632860.16835424X-RAY DIFFRACTION97.57
2.4-2.450.2132830.16925371X-RAY DIFFRACTION97.42
2.45-2.490.20662810.16985341X-RAY DIFFRACTION97.32
2.49-2.540.2342850.17275414X-RAY DIFFRACTION97.09
2.54-2.590.22132840.15395399X-RAY DIFFRACTION97.06
2.59-2.650.21942790.15315305X-RAY DIFFRACTION96.39
2.65-2.710.20612790.14965306X-RAY DIFFRACTION96.19
2.71-2.770.20052780.14485268X-RAY DIFFRACTION94.88
2.77-2.850.19742720.14655172X-RAY DIFFRACTION93.59
2.85-2.930.20632380.14714521X-RAY DIFFRACTION81.48
2.93-3.030.20292280.1524332X-RAY DIFFRACTION77.94
3.03-3.140.19852750.14565223X-RAY DIFFRACTION94.16
3.14-3.260.17742900.14735516X-RAY DIFFRACTION99.28
3.26-3.410.17582880.14615481X-RAY DIFFRACTION99
3.41-3.590.18342910.13945513X-RAY DIFFRACTION99.16
3.59-3.810.1612900.12935524X-RAY DIFFRACTION99.13
3.81-4.110.1522910.11955530X-RAY DIFFRACTION99.18
4.11-4.520.13352920.10875534X-RAY DIFFRACTION99.13
4.52-5.170.14552910.11645543X-RAY DIFFRACTION99.22
5.17-6.510.17032940.13785601X-RAY DIFFRACTION99.16
6.51-34.820.14682950.13255589X-RAY DIFFRACTION97.53

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