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- PDB-8r3r: Transketolase from Streptococcus pneumoniae in complex with thiam... -

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Basic information

Entry
Database: PDB / ID: 8r3r
TitleTransketolase from Streptococcus pneumoniae in complex with thiamin pyrophosphate
ComponentsProbable transketolase
KeywordsCYTOSOLIC PROTEIN / transketolase / pentose phosphate pathway / infectious organism
Function / homology
Function and homology information


transketolase / transketolase activity / DNA recombination / metal ion binding
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
THIAMINE DIPHOSPHATE / Probable transketolase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
A: Probable transketolase
B: Probable transketolase
C: Probable transketolase
D: Probable transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,29214
Polymers292,3704
Non-polymers1,92310
Water42,5872364
1
A: Probable transketolase
B: Probable transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,2088
Polymers146,1852
Non-polymers1,0236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-70 kcal/mol
Surface area42720 Å2
2
C: Probable transketolase
D: Probable transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0846
Polymers146,1852
Non-polymers8994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-74 kcal/mol
Surface area43010 Å2
Unit cell
Length a, b, c (Å)93.760, 119.130, 136.680
Angle α, β, γ (deg.)90.000, 106.460, 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

#1: Protein
Probable transketolase / TK


Mass: 73092.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: tkt, recP, SP_2030 / Production host: Escherichia coli (E. coli) / References: UniProt: P22976, transketolase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2364 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Li2Cl2, 0.1 M Tris pH 8.5, 28 % (w/v) PEG 6000

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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 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9676 Å / Relative weight: 1
ReflectionResolution: 2.35→34.05 Å / Num. obs: 118040 / % possible obs: 98.5 % / Redundancy: 7.07 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.991 / Net I/σ(I): 10.78
Reflection shellResolution: 2.35→2.4 Å / Num. unique obs: 7205 / CC1/2: 0.853

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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: 2.35→34.05 Å / SU ML: 0.2574 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 5903 5 %
Rwork0.1543 112137 -
obs0.1574 118040 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.33 Å2
Refinement stepCycle: LAST / Resolution: 2.35→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20047 0 116 2364 22527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010320617
X-RAY DIFFRACTIONf_angle_d0.977428062
X-RAY DIFFRACTIONf_chiral_restr0.05493101
X-RAY DIFFRACTIONf_plane_restr0.00753700
X-RAY DIFFRACTIONf_dihedral_angle_d6.88952869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.31571960.24113710X-RAY DIFFRACTION98.86
2.38-2.40.27511990.21293780X-RAY DIFFRACTION98.73
2.4-2.430.29471940.19023688X-RAY DIFFRACTION98.8
2.43-2.460.26411970.17763752X-RAY DIFFRACTION98.95
2.46-2.50.26661950.17593708X-RAY DIFFRACTION98.86
2.5-2.530.24691990.16983775X-RAY DIFFRACTION98.78
2.53-2.570.2581960.17373727X-RAY DIFFRACTION98.74
2.57-2.610.29011960.17963712X-RAY DIFFRACTION98.74
2.61-2.650.25741970.18223742X-RAY DIFFRACTION98.97
2.65-2.690.22731980.1613766X-RAY DIFFRACTION99.2
2.69-2.740.24731970.15993741X-RAY DIFFRACTION99.27
2.74-2.790.24541970.16143756X-RAY DIFFRACTION99.07
2.79-2.840.24711960.15923717X-RAY DIFFRACTION97.41
2.84-2.90.24741900.16943604X-RAY DIFFRACTION96.34
2.9-2.960.24131900.16923616X-RAY DIFFRACTION94.91
2.96-3.030.24711840.16263485X-RAY DIFFRACTION91.77
3.03-3.110.22281810.16643443X-RAY DIFFRACTION91.65
3.11-3.190.24851930.1663670X-RAY DIFFRACTION97.01
3.19-3.280.19972000.15353791X-RAY DIFFRACTION99.92
3.28-3.390.23882000.16153812X-RAY DIFFRACTION100
3.39-3.510.20822000.153797X-RAY DIFFRACTION100
3.51-3.650.19371990.14663775X-RAY DIFFRACTION100
3.65-3.820.18812000.13863809X-RAY DIFFRACTION99.98
3.82-4.020.19052000.13073794X-RAY DIFFRACTION99.97
4.02-4.270.15432010.12263813X-RAY DIFFRACTION100
4.27-4.60.1572000.11943805X-RAY DIFFRACTION100
4.6-5.060.15432020.12153834X-RAY DIFFRACTION100
5.06-5.790.17992000.13483800X-RAY DIFFRACTION100
5.79-7.280.20572020.15623848X-RAY DIFFRACTION100
7.28-34.050.1682040.14163867X-RAY DIFFRACTION99.05

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