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- PDB-5xqk: Crystal Structure of Transketolase in complex with xylulose-5-pho... -

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Basic information

Entry
Database: PDB / ID: 5xqk
TitleCrystal Structure of Transketolase in complex with xylulose-5-phosphate 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
DI(HYDROXYETHYL)ETHER / Chem-T5X / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)76,49310
Polymers75,0541
Non-polymers1,4389
Water13,583754
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,98620
Polymers150,1092
Non-polymers2,87718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area11130 Å2
ΔGint-63 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.709, 183.724, 98.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-T5X / 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol / D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT


Mass: 655.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H30N4O15P3S
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
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: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→30 Å / Num. obs: 312132 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.2
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 1.12→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.635 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13352 16024 4.9 %RANDOM
Rwork0.12252 ---
obs0.12305 312132 94.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0 Å2
2---0.15 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 90 756 5976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195479
X-RAY DIFFRACTIONr_bond_other_d0.0020.025190
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.977460
X-RAY DIFFRACTIONr_angle_other_deg1.0593.00211995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94524.775222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34715870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5821520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216276
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021204
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.5752785
X-RAY DIFFRACTIONr_mcbond_other0.8711.5742784
X-RAY DIFFRACTIONr_mcangle_it1.1282.3713507
X-RAY DIFFRACTIONr_mcangle_other1.1282.3723508
X-RAY DIFFRACTIONr_scbond_it1.3181.7872693
X-RAY DIFFRACTIONr_scbond_other1.3171.7872693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.562.5943953
X-RAY DIFFRACTIONr_long_range_B_refined2.54414.637118
X-RAY DIFFRACTIONr_long_range_B_other2.07613.6396628
X-RAY DIFFRACTIONr_rigid_bond_restr2.37310668
X-RAY DIFFRACTIONr_sphericity_free25.2185149
X-RAY DIFFRACTIONr_sphericity_bonded6.015511147
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 756 -
Rwork0.225 13751 -
obs--56.75 %

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