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- PDB-5hgx: Crystal Structure of Transketolase mutant - H261F from Pichia Stipitis -

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Basic information

Entry
Database: PDB / ID: 5hgx
TitleCrystal Structure of Transketolase mutant - H261F 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
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 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)75,3022
Polymers75,0631
Non-polymers2381
Water19,2401068
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,6044
Polymers150,1272
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area9120 Å2
ΔGint-46 kcal/mol
Surface area42460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.148, 184.556, 98.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

21A-967-

HOH

31A-1274-

HOH

41A-1539-

HOH

51A-1585-

HOH

61A-1704-

HOH

71A-1718-

HOH

81A-1829-

HOH

91A-1830-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 75063.484 Da / Num. of mol.: 1 / Mutation: H261F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1068 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, MES, NaCl / PH range: 6.3-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 315r / 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: 1.09→30 Å / Num. obs: 380091 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.95 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.163 / Net I/av σ(I): 18.948 / Net I/σ(I): 14.8 / Num. measured all: 1797707
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.09-1.133.50.513372121.16198.1
1.13-1.173.80.362378961.23199.8
1.17-1.234.20.287379631.264100
1.23-1.294.30.228380491.264100
1.29-1.374.40.187380861.242100
1.37-1.484.50.13380981.21100
1.48-1.634.70.102381811.173100
1.63-1.864.90.084382221.14599.9
1.86-2.355.50.055384191.037100
2.35-307.40.066379651.06397.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPU

1gpu


Resolution: 1.09→23.871 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 9.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1217 19112 5.03 %
Rwork0.1058 --
obs0.1066 380041 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.09→23.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 44 1068 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095444
X-RAY DIFFRACTIONf_angle_d1.1727417
X-RAY DIFFRACTIONf_dihedral_angle_d16.0691975
X-RAY DIFFRACTIONf_chiral_restr0.085822
X-RAY DIFFRACTIONf_plane_restr0.008968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0878-1.10020.23735520.223410782X-RAY DIFFRACTION90
1.1002-1.11310.21946040.199411876X-RAY DIFFRACTION98
1.1131-1.12670.1816660.176111843X-RAY DIFFRACTION99
1.1267-1.14090.17246720.159911935X-RAY DIFFRACTION99
1.1409-1.1560.17516510.147412088X-RAY DIFFRACTION100
1.156-1.17180.15456100.138712016X-RAY DIFFRACTION100
1.1718-1.18850.14736660.131412042X-RAY DIFFRACTION100
1.1885-1.20630.14756530.130312032X-RAY DIFFRACTION100
1.2063-1.22510.13476480.119512091X-RAY DIFFRACTION100
1.2251-1.24520.13136610.111612028X-RAY DIFFRACTION100
1.2452-1.26670.12246430.106812087X-RAY DIFFRACTION100
1.2667-1.28970.12076290.102312056X-RAY DIFFRACTION100
1.2897-1.31450.12046430.100312106X-RAY DIFFRACTION100
1.3145-1.34130.11396020.099412070X-RAY DIFFRACTION100
1.3413-1.37050.11766090.097212122X-RAY DIFFRACTION100
1.3705-1.40240.11086540.091812106X-RAY DIFFRACTION100
1.4024-1.43740.10586180.089712065X-RAY DIFFRACTION100
1.4374-1.47630.1035880.085112185X-RAY DIFFRACTION100
1.4763-1.51970.09966140.08312140X-RAY DIFFRACTION100
1.5197-1.56880.10256140.081512141X-RAY DIFFRACTION100
1.5688-1.62480.10026750.079112074X-RAY DIFFRACTION100
1.6248-1.68990.09546700.080912088X-RAY DIFFRACTION100
1.6899-1.76680.10766780.086812089X-RAY DIFFRACTION100
1.7668-1.85990.10446770.089712115X-RAY DIFFRACTION100
1.8599-1.97640.10116450.088712187X-RAY DIFFRACTION100
1.9764-2.12890.10346220.090712179X-RAY DIFFRACTION100
2.1289-2.34290.11286480.090912222X-RAY DIFFRACTION100
2.3429-2.68160.10776380.09712265X-RAY DIFFRACTION100
2.6816-3.3770.12576570.115112266X-RAY DIFFRACTION100
3.377-23.87660.15066050.133311633X-RAY DIFFRACTION92

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