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- PDB-5i5e: Crystal Structure of Transketolase mutants-H66/261C complex with ... -

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Basic information

Entry
Database: PDB / ID: 5i5e
TitleCrystal Structure of Transketolase mutants-H66/261C complex with xylulose-5-phoaphate from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / Transketolase / xylulose-5-phosphate
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
5-O-phosphono-D-xylulose / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)75,6804
Polymers74,9841
Non-polymers6963
Water13,998777
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,3608
Polymers149,9692
Non-polymers1,3916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11200 Å2
ΔGint-89 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.885, 182.084, 98.263
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-1066-

HOH

31A-1499-

HOH

41A-1516-

HOH

51A-1562-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 74984.438 Da / Num. of mol.: 1 / Mutation: H66C, H261C
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: Sugar ChemComp-5SP / 5-O-phosphono-D-xylulose / D-xylulose 5-phosphate


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 777 / 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: 59.98 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. obs: 113628 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.24 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.248 / Net I/av σ(I): 14.402 / Net I/σ(I): 9.9 / Num. measured all: 559503
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.62-1.684.40.721100
1.68-1.754.50.5881100
1.75-1.824.50.454199.9
1.82-1.924.50.328199.9
1.92-2.044.70.258199.9
2.04-2.250.199199.9
2.2-2.425.30.151199.9
2.42-2.775.40.112199.7
2.77-3.495.40.083199.7
3.49-305.60.081199.3

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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: 1.62→23.839 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.53
RfactorNum. reflection% reflection
Rfree0.1815 5686 5.02 %
Rwork0.158 --
obs0.1592 113342 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.43 Å2 / Biso mean: 27.073 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 1.62→23.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 66 777 5971
Biso mean--44.9 37.37 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125314
X-RAY DIFFRACTIONf_angle_d1.2047226
X-RAY DIFFRACTIONf_chiral_restr0.064807
X-RAY DIFFRACTIONf_plane_restr0.009937
X-RAY DIFFRACTIONf_dihedral_angle_d11.5123148
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 (%)
1.6165-1.63490.23231700.21183204337489
1.6349-1.65410.24722030.206235723775100
1.6541-1.67430.24681970.194335843781100
1.6743-1.69550.24522030.197535513754100
1.6955-1.71780.21612020.19635763778100
1.7178-1.74130.24381820.188235783760100
1.7413-1.76620.23731950.180936053800100
1.7662-1.79250.21131790.182535983777100
1.7925-1.82050.21391870.173635793766100
1.8205-1.85040.21632050.179435653770100
1.8504-1.88230.22251950.166835753770100
1.8823-1.91650.19661980.167335773775100
1.9165-1.95330.22441900.167235843774100
1.9533-1.99320.21291850.170735883773100
1.9932-2.03650.19611680.168236173785100
2.0365-2.08380.1931900.163835853775100
2.0838-2.13590.1951820.164735763758100
2.1359-2.19360.1831720.160136143786100
2.1936-2.25810.20211750.15813605378099
2.2581-2.33090.18062120.15883550376299
2.3309-2.41420.18591870.15583614380199
2.4142-2.51070.16781970.15423558375599
2.5107-2.62490.16951810.15713573375499
2.6249-2.76310.17711950.15043587378299
2.7631-2.93590.18481700.1573639380999
2.9359-3.16210.18781940.16043597379199
3.1621-3.47940.17782010.157636453846100
3.4794-3.98090.14781980.139736673865100
3.9809-5.00790.1441740.12933692386699
5.0079-23.84130.17711990.16853801400099

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