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- PDB-5i5g: Crystal Structure of Transketolase mutant-R525L from Pichia Stipitis -

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Basic information

Entry
Database: PDB / ID: 5i5g
TitleCrystal Structure of Transketolase mutant-R525L 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 / PYROPHOSPHATE 2- / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 15, 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

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2923
Polymers75,0101
Non-polymers2822
Water6,485360
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,5856
Polymers150,0212
Non-polymers5644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10090 Å2
ΔGint-43 kcal/mol
Surface area41560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.121, 184.543, 98.170
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-977-

HOH

21A-1069-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 75010.414 Da / Num. of mol.: 1 / Mutation: R525L
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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 60.95 %
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: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 67032 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 20.41 Å2 / Rmerge(I) obs: 0.155 / Net I/av σ(I): 14.057 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-1.988.30.9461100
1.98-2.028.40.8331100
2.02-2.068.40.7871100
2.06-2.18.30.641100
2.1-2.158.40.5491100
2.15-2.28.40.4811100
2.2-2.258.30.4311100
2.25-2.318.40.371100
2.31-2.388.40.3111100
2.38-2.468.40.2711100
2.46-2.548.40.2361100
2.54-2.658.40.211100
2.65-2.778.40.1841100
2.77-2.918.40.151100
2.91-3.098.40.1331100
3.09-3.338.20.1191100
3.33-3.677.90.0991100
3.67-4.27.90.081100
4.2-5.288.20.0551100
5.28-307.90.049199.9

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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: 1.95→29.56 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.83
RfactorNum. reflection% reflection
Rfree0.1862 3334 5.03 %
Rwork0.1606 --
obs0.1618 66321 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.79 Å2 / Biso mean: 25.0973 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.95→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 26 360 5519
Biso mean--40.82 30.02 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085273
X-RAY DIFFRACTIONf_angle_d0.9027173
X-RAY DIFFRACTIONf_chiral_restr0.054804
X-RAY DIFFRACTIONf_plane_restr0.006931
X-RAY DIFFRACTIONf_dihedral_angle_d11.7773123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9496-1.97750.26371350.21652209234485
1.9775-2.0070.25021440.20092444258893
2.007-2.03840.24521420.20112508265097
2.0384-2.07180.20871440.18492607275198
2.0718-2.10750.19831620.1772589275199
2.1075-2.14580.18991440.166126092753100
2.1458-2.18710.22411590.165526162775100
2.1871-2.23170.18561300.156126222752100
2.2317-2.28020.19391060.159226932799100
2.2802-2.33320.16191220.140626192741100
2.3332-2.39150.19461340.137426722806100
2.3915-2.45620.1721580.134125972755100
2.4562-2.52840.19831540.138126462800100
2.5284-2.610.17961250.141526582783100
2.61-2.70320.17281310.139226402771100
2.7032-2.81130.17291520.137226432795100
2.8113-2.93920.16091340.140826662800100
2.9392-3.0940.18311530.147426462799100
3.094-3.28760.18231160.150626892805100
3.2876-3.5410.1861070.157926952802100
3.541-3.89670.15581320.154327052837100
3.8967-4.45890.15071210.158127092830100
4.4589-5.61140.19391510.173327162867100
5.6114-29.56350.19871780.204127892967100

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