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

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Basic information

Entry
Database: PDB / ID: 5xsa
TitleCrystal Structure of Transketolase in complex with TPP intermediate III 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-8EL / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.975 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 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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)75,5213
Polymers75,0541
Non-polymers4662
Water17,258958
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0426
Polymers150,1092
Non-polymers9334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8930 Å2
ΔGint-45 kcal/mol
Surface area41110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.272, 185.469, 98.917
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-817-

HOH

21A-1547-

HOH

31A-1620-

HOH

41A-1737-

HOH

51A-1751-

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-8EL / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 958 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
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: 0.7 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.89→30 Å / Num. obs: 690531 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.9
Reflection shellRmerge(I) obs: 0.64

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Processing

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

5hyv


Resolution: 0.975→29.628 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.87
RfactorNum. reflection% reflection
Rfree0.1534 26484 5.03 %
Rwork0.1415 --
obs0.1421 526412 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.975→29.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 27 958 6115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115442
X-RAY DIFFRACTIONf_angle_d1.2877437
X-RAY DIFFRACTIONf_dihedral_angle_d6.5733113
X-RAY DIFFRACTIONf_chiral_restr0.15830
X-RAY DIFFRACTIONf_plane_restr0.01975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9745-0.98560.18948610.168615517X-RAY DIFFRACTION92
0.9856-0.99720.18318240.15916182X-RAY DIFFRACTION95
0.9972-1.00930.17818390.155316320X-RAY DIFFRACTION97
1.0093-1.02210.16768370.148716524X-RAY DIFFRACTION98
1.0221-1.03560.15878210.147616756X-RAY DIFFRACTION99
1.0356-1.04970.15159090.144216643X-RAY DIFFRACTION99
1.0497-1.06470.16378760.141516740X-RAY DIFFRACTION99
1.0647-1.08060.1548680.136616693X-RAY DIFFRACTION99
1.0806-1.09750.15479260.134916602X-RAY DIFFRACTION99
1.0975-1.11550.14969790.131416572X-RAY DIFFRACTION99
1.1155-1.13480.14138580.128916702X-RAY DIFFRACTION99
1.1348-1.15540.13458240.125116734X-RAY DIFFRACTION99
1.1554-1.17760.14248840.125316714X-RAY DIFFRACTION99
1.1776-1.20170.14638610.122916671X-RAY DIFFRACTION99
1.2017-1.22780.14228700.123216664X-RAY DIFFRACTION99
1.2278-1.25630.13018740.123816637X-RAY DIFFRACTION99
1.2563-1.28780.13899250.124116772X-RAY DIFFRACTION99
1.2878-1.32260.13699290.125816765X-RAY DIFFRACTION99
1.3226-1.36150.14998650.13116823X-RAY DIFFRACTION99
1.3615-1.40540.1388680.127116884X-RAY DIFFRACTION99
1.4054-1.45570.13659400.124816711X-RAY DIFFRACTION99
1.4557-1.5140.13018500.121316831X-RAY DIFFRACTION99
1.514-1.58290.13059220.119616690X-RAY DIFFRACTION99
1.5829-1.66630.13919190.122716718X-RAY DIFFRACTION98
1.6663-1.77070.13458470.131716700X-RAY DIFFRACTION98
1.7707-1.90740.15489310.138816587X-RAY DIFFRACTION98
1.9074-2.09930.14368780.137116573X-RAY DIFFRACTION97
2.0993-2.40290.14929050.141416894X-RAY DIFFRACTION99
2.4029-3.0270.16438770.150817096X-RAY DIFFRACTION99
3.027-29.64190.16519170.151617213X-RAY DIFFRACTION98

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