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- PDB-5xu9: Crystal Structure of Transketolase in complex with TPP intermedia... -

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Basic information

Entry
Database: PDB / ID: 5xu9
TitleCrystal Structure of Transketolase in complex with TPP intermediate IX and gauche form erythrose-4-phosphate from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / nucleus / metal ion binding / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. ...Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / 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-8N9 / ERYTHOSE-4-PHOSPHATE / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.166 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Chembiochem / Year: 2018
Title: Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Ke, S.C. / Lyu, S.Y. / Hsu, L.J. / Li, Y.S. / Chen, S.C. / Wang, K.C. / Li, T.L.
History
DepositionJun 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,52211
Polymers75,0541
Non-polymers1,46710
Water13,241735
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,04422
Polymers150,1092
Non-polymers2,93520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13410 Å2
ΔGint-34 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.259, 186.041, 98.667
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-1442-

HOH

21A-1533-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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 (E. coli) / References: UniProt: P34736, transketolase
#5: Sugar ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O7P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 744 molecules

#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.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8N9 / 2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[1,2-bis(oxidanyl)ethylidene]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate / (E)-2(3-((4-amino-2-methylpyrimidin-5-yl)methyl)-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydrothiazol-5-yl)ethyl trihydrogen diphosphate


Mass: 484.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N4O9P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
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: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. obs: 307358 / % possible obs: 95.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.45

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Processing

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

5hyv


Resolution: 1.166→19.61 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.54
RfactorNum. reflection% reflection
Rfree0.1659 14987 5 %
Rwork0.1462 --
obs0.1472 299493 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.166→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 92 735 5957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135434
X-RAY DIFFRACTIONf_angle_d1.5057388
X-RAY DIFFRACTIONf_dihedral_angle_d4.0833096
X-RAY DIFFRACTIONf_chiral_restr0.16822
X-RAY DIFFRACTIONf_plane_restr0.01954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.166-1.17930.22864220.20898956X-RAY DIFFRACTION90
1.1793-1.19310.2264450.20428923X-RAY DIFFRACTION90
1.1931-1.20770.23784310.20728976X-RAY DIFFRACTION91
1.2077-1.2230.23754850.19968953X-RAY DIFFRACTION91
1.223-1.2390.21315030.18598987X-RAY DIFFRACTION91
1.239-1.2560.19955130.18559053X-RAY DIFFRACTION92
1.256-1.2740.20954880.17879091X-RAY DIFFRACTION92
1.274-1.2930.19075010.17929122X-RAY DIFFRACTION92
1.293-1.31320.2045400.17199092X-RAY DIFFRACTION93
1.3132-1.33470.18324930.1649235X-RAY DIFFRACTION93
1.3347-1.35770.17375220.16099224X-RAY DIFFRACTION94
1.3577-1.38240.18264790.15919268X-RAY DIFFRACTION94
1.3824-1.4090.19625200.15459390X-RAY DIFFRACTION95
1.409-1.43770.17945200.15229373X-RAY DIFFRACTION95
1.4377-1.4690.17224770.13869557X-RAY DIFFRACTION96
1.469-1.50310.15644600.13499698X-RAY DIFFRACTION97
1.5031-1.54070.14645430.11629841X-RAY DIFFRACTION100
1.5407-1.58230.13955330.11249887X-RAY DIFFRACTION100
1.5823-1.62890.13975490.11349894X-RAY DIFFRACTION100
1.6289-1.68140.14335360.11659926X-RAY DIFFRACTION100
1.6814-1.74150.13595390.11659890X-RAY DIFFRACTION100
1.7415-1.81120.15145300.11999920X-RAY DIFFRACTION100
1.8112-1.89350.15295350.12529903X-RAY DIFFRACTION100
1.8935-1.99330.15934890.13159993X-RAY DIFFRACTION100
1.9933-2.1180.14644760.13259993X-RAY DIFFRACTION99
2.118-2.28130.15785470.13499810X-RAY DIFFRACTION99
2.2813-2.51050.17485070.14279797X-RAY DIFFRACTION98
2.5105-2.87280.16784400.1579686X-RAY DIFFRACTION96
2.8728-3.61570.17114660.16069794X-RAY DIFFRACTION96
3.6157-19.61240.17114980.15799274X-RAY DIFFRACTION90

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