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- PDB-5xtv: Crystal Structure of Transketolase in complex with TPP intermedia... -

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Basic information

Entry
Database: PDB / ID: 5xtv
TitleCrystal Structure of Transketolase in complex with TPP intermediate V from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / nucleus / 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, 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, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8EF / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.931 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Lyu, S.Y. / Hsu, L.J. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8396
Polymers75,0541
Non-polymers7855
Water17,709983
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,67812
Polymers150,1092
Non-polymers1,57010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10320 Å2
ΔGint-32 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.023, 184.583, 99.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-821-

HOH

21A-1588-

HOH

31A-1769-

HOH

41A-1780-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 75054.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8EF / 2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate


Mass: 426.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 983 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.93→30 Å / Num. obs: 609263 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.6
Reflection shellRmerge(I) obs: 0.692

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 0.931→28.412 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.62
RfactorNum. reflection% reflection
Rfree0.1399 30316 4.98 %
Rwork0.1307 --
obs0.1312 609263 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.931→28.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 48 983 6161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115426
X-RAY DIFFRACTIONf_angle_d1.3197401
X-RAY DIFFRACTIONf_dihedral_angle_d6.6553117
X-RAY DIFFRACTIONf_chiral_restr0.141826
X-RAY DIFFRACTIONf_plane_restr0.01966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9306-0.94120.21169270.215118448X-RAY DIFFRACTION96
0.9412-0.95220.21669680.195119076X-RAY DIFFRACTION99
0.9522-0.96380.20169550.185119232X-RAY DIFFRACTION99
0.9638-0.9760.19949980.174219087X-RAY DIFFRACTION99
0.976-0.98890.168410290.160919138X-RAY DIFFRACTION100
0.9889-1.00240.165910020.153619211X-RAY DIFFRACTION100
1.0024-1.01680.15589860.140319148X-RAY DIFFRACTION100
1.0168-1.03190.137210300.129119327X-RAY DIFFRACTION100
1.0319-1.04810.1339990.122919169X-RAY DIFFRACTION100
1.0481-1.06520.126810260.113419246X-RAY DIFFRACTION100
1.0652-1.08360.117610180.107219216X-RAY DIFFRACTION100
1.0836-1.10330.113410430.10319270X-RAY DIFFRACTION100
1.1033-1.12450.112610290.100819233X-RAY DIFFRACTION100
1.1245-1.14750.108510460.097419258X-RAY DIFFRACTION100
1.1475-1.17240.111310070.095819299X-RAY DIFFRACTION100
1.1724-1.19970.103510100.095419292X-RAY DIFFRACTION100
1.1997-1.22970.112410190.098819311X-RAY DIFFRACTION100
1.2297-1.2630.110310540.100319262X-RAY DIFFRACTION100
1.263-1.30010.11259610.101319406X-RAY DIFFRACTION100
1.3001-1.34210.11739600.103819364X-RAY DIFFRACTION100
1.3421-1.39010.118210100.107819364X-RAY DIFFRACTION100
1.3901-1.44570.11910690.109819318X-RAY DIFFRACTION100
1.4457-1.51150.11910460.109619306X-RAY DIFFRACTION100
1.5115-1.59120.12429780.111419443X-RAY DIFFRACTION100
1.5912-1.69090.13329850.119219403X-RAY DIFFRACTION100
1.6909-1.82140.137510470.133719417X-RAY DIFFRACTION100
1.8214-2.00470.14169790.138319512X-RAY DIFFRACTION100
2.0047-2.29460.143110620.137419518X-RAY DIFFRACTION100
2.2946-2.89060.152410490.151819613X-RAY DIFFRACTION100
2.8906-28.42560.172310240.157620060X-RAY DIFFRACTION100

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