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- PDB-5xvt: Crystal Structure of Transketolase in complex with hydroxylated T... -

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Basic information

Entry
Database: PDB / ID: 5xvt
TitleCrystal Structure of Transketolase in complex with hydroxylated TPP from Pichia Stipitis, crystal 2
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


purine nucleotide metabolic process / transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / 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-8FL / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.85 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 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)76,28010
Polymers75,0541
Non-polymers1,2259
Water16,141896
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,55920
Polymers150,1092
Non-polymers2,45018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12410 Å2
ΔGint-27 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.220, 185.340, 99.170
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-829-

HOH

21A-850-

HOH

31A-1238-

HOH

41A-1537-

HOH

51A-1580-

HOH

61A-1654-

HOH

71A-1686-

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 (E. coli) / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-8FL / 2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 442.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O8P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 60.3 %
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: NSRRC / Beamline: TPS 05A / Wavelength: 0.7 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.85→30 Å / Num. obs: 805990 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 0.85→0.9 Å / Rmerge(I) obs: 0.81

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
RefinementResolution: 0.85→27.676 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1385 39851 4.95 %
Rwork0.1325 --
obs0.1328 805570 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.85→27.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 77 896 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115366
X-RAY DIFFRACTIONf_angle_d1.3157293
X-RAY DIFFRACTIONf_dihedral_angle_d15.7221968
X-RAY DIFFRACTIONf_chiral_restr0.295815
X-RAY DIFFRACTIONf_plane_restr0.01942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.85960.286813200.283225224X-RAY DIFFRACTION99
0.8596-0.86980.272113410.265925371X-RAY DIFFRACTION100
0.8698-0.88040.252814290.249925388X-RAY DIFFRACTION100
0.8804-0.89150.253212820.238725362X-RAY DIFFRACTION100
0.8915-0.90320.218714130.226325363X-RAY DIFFRACTION100
0.9032-0.91560.21613520.212925319X-RAY DIFFRACTION100
0.9156-0.92870.196512670.196125536X-RAY DIFFRACTION100
0.9287-0.94260.194513630.187725401X-RAY DIFFRACTION100
0.9426-0.95730.184412410.169425472X-RAY DIFFRACTION100
0.9573-0.9730.163512810.156525554X-RAY DIFFRACTION100
0.973-0.98980.148112890.140225415X-RAY DIFFRACTION100
0.9898-1.00780.140112600.129525498X-RAY DIFFRACTION100
1.0078-1.02710.125913240.116925506X-RAY DIFFRACTION100
1.0271-1.04810.117213770.109125369X-RAY DIFFRACTION100
1.0481-1.07090.107112880.099425534X-RAY DIFFRACTION100
1.0709-1.09580.101613120.092525486X-RAY DIFFRACTION100
1.0958-1.12320.094813080.087725553X-RAY DIFFRACTION100
1.1232-1.15360.092413180.084225459X-RAY DIFFRACTION100
1.1536-1.18750.093712840.083225565X-RAY DIFFRACTION100
1.1875-1.22590.093112890.085725509X-RAY DIFFRACTION100
1.2259-1.26970.096112580.087525608X-RAY DIFFRACTION100
1.2697-1.32050.098712970.091425599X-RAY DIFFRACTION100
1.3205-1.38060.103813320.09725532X-RAY DIFFRACTION100
1.3806-1.45340.104613520.098425529X-RAY DIFFRACTION100
1.4534-1.54440.104714310.098925553X-RAY DIFFRACTION100
1.5444-1.66370.117313650.109525600X-RAY DIFFRACTION100
1.6637-1.83110.13313320.127225679X-RAY DIFFRACTION100
1.8311-2.0960.141413700.134325717X-RAY DIFFRACTION100
2.096-2.64040.153713990.146925830X-RAY DIFFRACTION100
2.6404-27.69070.153913770.155526188X-RAY DIFFRACTION99

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