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- PDB-5xps: Crystal Structure of Transketolase in complex with erythrose-4-ph... -

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Basic information

Entry
Database: PDB / ID: 5xps
TitleCrystal Structure of Transketolase in complex with erythrose-4-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
ERYTHOSE-4-PHOSPHATE / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 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)76,1448
Polymers75,0541
Non-polymers1,0907
Water16,970942
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,28916
Polymers150,1092
Non-polymers2,18014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13450 Å2
ΔGint-54 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.149, 185.246, 98.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase
#4: Sugar ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O7P

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Non-polymers , 4 types, 948 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG400

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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: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.07→92.62 Å / Num. obs: 403372 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.058 / Rsym value: 0.07 / Net I/σ(I): 20.7
Reflection shellHighest resolution: 1.07 Å / Rsym value: 0.73

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Processing

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

5hyv


Resolution: 1.07→92.62 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.596 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13154 19091 4.9 %RANDOM
Rwork0.11854 ---
obs0.11919 368116 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.413 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0 Å2
2---0.41 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.07→92.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 67 948 6145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195423
X-RAY DIFFRACTIONr_bond_other_d0.0020.025131
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9677389
X-RAY DIFFRACTIONr_angle_other_deg1.286311854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78124.798223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56215863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8631520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216228
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021201
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_it3.041.6582759
X-RAY DIFFRACTIONr_mcbond_other3.041.6582758
X-RAY DIFFRACTIONr_mcangle_it3.2632.4883467
X-RAY DIFFRACTIONr_mcangle_other3.2632.4883468
X-RAY DIFFRACTIONr_scbond_it2.8721.8532663
X-RAY DIFFRACTIONr_scbond_other2.8721.8532663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3592.6983918
X-RAY DIFFRACTIONr_long_range_B_refined4.30816.0217296
X-RAY DIFFRACTIONr_long_range_B_other4.30816.0217296
X-RAY DIFFRACTIONr_rigid_bond_restr4.078310553
X-RAY DIFFRACTIONr_sphericity_free35.0285199
X-RAY DIFFRACTIONr_sphericity_bonded11.958511174
LS refinement shellResolution: 1.069→1.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 781 -
Rwork0.197 15903 -
obs--56.02 %

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