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- PDB-5i51: Crystal Structure of Transketolase mutant-R356L complex with fruc... -

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Basic information

Entry
Database: PDB / ID: 5i51
TitleCrystal Structure of Transketolase mutant-R356L complex with fructose-6-phoaphate from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / fructose-6-phosphate / thiamine diphosphate
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
FRUCTOSE -6-PHOSPHATE / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 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

Downloads & links

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1608
Polymers75,0101
Non-polymers1,1507
Water9,890549
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,32116
Polymers150,0212
Non-polymers2,30014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13470 Å2
ΔGint-64 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.828, 183.248, 98.749
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-819-

HOH

21A-1198-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transketolase / TK


Mass: 75010.414 Da / Num. of mol.: 1 / Mutation: R356L
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

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Non-polymers , 5 types, 556 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, NaCl, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 134744 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 13.27 Å2 / Rmerge(I) obs: 0.069 / Net I/av σ(I): 29.27 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.54-1.577.70.9051100
1.57-1.67.80.7751100
1.6-1.637.90.6811100
1.63-1.667.90.61100
1.66-1.6980.5091100
1.69-1.7380.4451100
1.73-1.788.10.3611100
1.78-1.838.20.3041100
1.83-1.888.20.241100
1.88-1.948.20.1961100
1.94-2.018.30.1581100
2.01-2.098.20.1311100
2.09-2.198.20.1141100
2.19-2.38.10.1021100
2.3-2.447.90.091100
2.44-2.637.80.081100
2.63-2.980.0651100
2.9-3.328.30.041100
3.32-4.188.30.031100
4.18-308.10.026199.7

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Processing

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

1gpu


Resolution: 1.54→24.424 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.42
RfactorNum. reflection% reflection
Rfree0.1589 6451 4.88 %
Rwork0.1411 --
obs0.142 132249 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.58 Å2 / Biso mean: 18.8548 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: final / Resolution: 1.54→24.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 138 549 5820
Biso mean--42.9 29.96 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115448
X-RAY DIFFRACTIONf_angle_d1.1887415
X-RAY DIFFRACTIONf_chiral_restr0.064821
X-RAY DIFFRACTIONf_plane_restr0.008968
X-RAY DIFFRACTIONf_dihedral_angle_d11.1553224
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 (%)
1.5395-1.5570.2441660.21873158332475
1.557-1.57530.21131740.2013574374884
1.5753-1.59450.221990.20163855405491
1.5945-1.61470.19821950.19574106430197
1.6147-1.63590.2182260.1924192441899
1.6359-1.65830.20642130.18434187440099
1.6583-1.6820.20832050.176942594464100
1.682-1.70710.20472190.17342314450100
1.7071-1.73380.19331880.170643014489100
1.7338-1.76220.19962130.158842164429100
1.7622-1.79260.18932240.150442384462100
1.7926-1.82510.17212430.144742244467100
1.8251-1.86020.16282390.137642294468100
1.8602-1.89820.14342200.130842454465100
1.8982-1.93940.15711860.130443054491100
1.9394-1.98450.1462030.127942384441100
1.9845-2.03420.13822070.12842434450100
2.0342-2.08910.15442080.123343094517100
2.0891-2.15060.14432160.122642704486100
2.1506-2.21990.15872330.1242294462100
2.2199-2.29920.14112540.117242344488100
2.2992-2.39120.1442090.117342964505100
2.3912-2.49990.12192080.118842754483100
2.4999-2.63160.15312360.123442774513100
2.6316-2.79620.15232530.126142574510100
2.7962-3.01180.14622260.129343074533100
3.0118-3.31420.15572280.136642984526100
3.3142-3.79220.13352390.136943234562100
3.7922-4.7720.14841990.13643994598100
4.772-24.42690.18272220.176945234745100

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