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- PDB-5hyv: Crystal Structure of Transketolase with ThDP from Pichia Stipitis -

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Basic information

Entry
Database: PDB / ID: 5hyv
TitleCrystal Structure of Transketolase with ThDP 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, 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
THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.031 Å
AuthorsLi, T.L. / Hsu, L.J. / Hsu, N.S.
CitationJournal: Protein Eng. Des. Sel. / Year: 2016
Title: Structural and biochemical interrogation on transketolase from Pichia stipitis for new functionality
Authors: Hsu, L.J. / Hsu, N.S. / Wang, Y.L. / Wu, C.J. / Li, T.L.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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)75,9965
Polymers75,0541
Non-polymers9424
Water16,195899
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,99310
Polymers150,1092
Non-polymers1,8848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10680 Å2
ΔGint-85 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.762, 183.830, 98.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-820-

HOH

21A-877-

HOH

31A-1239-

HOH

41A-1509-

HOH

51A-1593-

HOH

61A-1605-

HOH

71A-1674-

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-TPP / THIAMINE DIPHOSPHATE


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES, NaCl, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.03→30 Å / Num. obs: 443954 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 10.42 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.147 / Net I/av σ(I): 18.787 / Net I/σ(I): 16 / Num. measured all: 3096480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.03-1.075.20.686439011.21398.9
1.07-1.115.40.442440861.27199.2
1.11-1.165.70.303442611.27699.5
1.16-1.2260.229443191.299.6
1.22-1.36.40.171444891.16599.9
1.3-1.46.80.127446171.184100
1.4-1.547.30.092445961.106100
1.54-1.767.40.099447441.153100
1.76-2.2290.083449171.059100
2.22-3010.50.064440241.03396.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2152: ???)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPU

1gpu


Resolution: 1.031→27.603 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.29
RfactorNum. reflection% reflection
Rfree0.1163 21545 4.85 %
Rwork0.1056 --
obs0.1062 443906 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.04 Å2 / Biso mean: 15.3387 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.031→27.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 119 899 6154
Biso mean--36.65 28.08 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095476
X-RAY DIFFRACTIONf_angle_d1.1647458
X-RAY DIFFRACTIONf_chiral_restr0.085826
X-RAY DIFFRACTIONf_plane_restr0.008973
X-RAY DIFFRACTIONf_dihedral_angle_d14.9331984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0306-1.04230.26926940.2559136381433297
1.0423-1.05460.23297260.228139551468199
1.0546-1.06740.19637240.1939139711469599
1.0674-1.08090.17826330.1693140421467599
1.0809-1.09520.16237240.1503140181474299
1.0952-1.11020.15026760.1346139981467499
1.1102-1.1260.12697290.119140631479299
1.126-1.14280.12247280.1091398514713100
1.1428-1.16070.1187200.10411405814778100
1.1607-1.17970.11787200.09961406014780100
1.1797-1.20010.1137270.09841407114798100
1.2001-1.22190.11296840.09851411014794100
1.2219-1.24540.11517130.10021409214805100
1.2454-1.27080.10557540.09021406214816100
1.2708-1.29840.10067660.08621410114867100
1.2984-1.32860.09797190.08611410914828100
1.3286-1.36190.09587190.08461419514914100
1.3619-1.39870.09887630.08351412314886100
1.3987-1.43980.09237260.08021413814864100
1.4398-1.48630.09387070.07851418214889100
1.4863-1.53940.09067360.07791412314859100
1.5394-1.60110.09927400.08441421214952100
1.6011-1.67390.09326910.0821420814899100
1.6739-1.76210.09896630.08971425914922100
1.7621-1.87250.10247230.09411425714980100
1.8725-2.01710.09797550.09321421514970100
2.0171-2.220.16990.09421427514974100
2.22-2.5410.10516870.09891434515032100
2.541-3.20060.13247590.1207142251498499
3.2006-27.61240.13917400.1289132711401190

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