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- PDB-5xt4: Crystal Structure of Transketolase in complex with TPP intermedia... -

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Basic information

Entry
Database: PDB / ID: 5xt4
TitleCrystal Structure of Transketolase in complex with TPP intermediate VIII' from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


purine nucleotide metabolic process / carbohydrate derivative metabolic process / transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / 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
DI(HYDROXYETHYL)ETHER / Chem-T6F / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 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

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0986
Polymers75,0541
Non-polymers1,0445
Water12,466692
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,19712
Polymers150,1092
Non-polymers2,08810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12790 Å2
ΔGint-66 kcal/mol
Surface area40740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.104, 184.934, 98.918
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-1158-

HOH

21A-1387-

HOH

31A-1488-

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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-T6F / 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-6-O-phosphono-D-glucitol / D-FRUCTOSE-6-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT


Mass: 685.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32N4O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 60.07 %
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→30 Å / Num. obs: 408728 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 26
Reflection shellRmerge(I) obs: 0.56

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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: 1.06→25.561 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.44
RfactorNum. reflection% reflection
Rfree0.144 20354 4.98 %
Rwork0.1351 --
obs0.1355 408728 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.06→25.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 64 692 5886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095514
X-RAY DIFFRACTIONf_angle_d1.2167542
X-RAY DIFFRACTIONf_dihedral_angle_d3.8213118
X-RAY DIFFRACTIONf_chiral_restr0.094839
X-RAY DIFFRACTIONf_plane_restr0.01983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0594-1.07140.26575080.23419386X-RAY DIFFRACTION72
1.0714-1.0840.21426660.198211411X-RAY DIFFRACTION88
1.084-1.09730.19237030.178312574X-RAY DIFFRACTION96
1.0973-1.11120.17567250.161812868X-RAY DIFFRACTION99
1.1112-1.12580.1596670.148812930X-RAY DIFFRACTION99
1.1258-1.14120.15736710.139113100X-RAY DIFFRACTION100
1.1412-1.15750.14676870.128113086X-RAY DIFFRACTION100
1.1575-1.17480.14296560.118613094X-RAY DIFFRACTION100
1.1748-1.19310.13876710.113613116X-RAY DIFFRACTION100
1.1931-1.21270.13427090.109813068X-RAY DIFFRACTION100
1.2127-1.23360.12296800.1113105X-RAY DIFFRACTION100
1.2336-1.2560.1237000.10913108X-RAY DIFFRACTION100
1.256-1.28020.13427020.109713082X-RAY DIFFRACTION100
1.2802-1.30630.12636730.107813081X-RAY DIFFRACTION100
1.3063-1.33470.12816470.105613203X-RAY DIFFRACTION100
1.3347-1.36580.11896640.104513114X-RAY DIFFRACTION100
1.3658-1.39990.12246620.104413167X-RAY DIFFRACTION100
1.3999-1.43780.11866770.102213104X-RAY DIFFRACTION100
1.4378-1.48010.1187170.101713115X-RAY DIFFRACTION100
1.4801-1.52790.1167120.101413142X-RAY DIFFRACTION100
1.5279-1.58250.11266410.102213182X-RAY DIFFRACTION100
1.5825-1.64580.11766440.108413217X-RAY DIFFRACTION100
1.6458-1.72070.14557060.118713173X-RAY DIFFRACTION100
1.7207-1.81140.13146650.124213201X-RAY DIFFRACTION100
1.8114-1.92480.14466740.128713217X-RAY DIFFRACTION100
1.9248-2.07340.13747670.132613153X-RAY DIFFRACTION100
2.0734-2.28190.14347070.132613247X-RAY DIFFRACTION100
2.2819-2.61190.14677210.143213268X-RAY DIFFRACTION100
2.6119-3.28960.16736810.160113354X-RAY DIFFRACTION100
3.2896-25.56830.14756510.145913508X-RAY DIFFRACTION98

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