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- PDB-5i4i: Crystal Structure of Transketolase from Pichia Stipitis -

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Basic information

Entry
Database: PDB / ID: 5i4i
TitleCrystal Structure of Transketolase from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / TKL
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
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_detector / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
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


Theoretical massNumber of molelcules
Total (without water)75,0541
Polymers75,0541
Non-polymers00
Water15,277848
1
A: Transketolase

A: Transketolase


Theoretical massNumber of molelcules
Total (without water)150,1092
Polymers150,1092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8550 Å2
ΔGint-44 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.546, 185.506, 98.876
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-1108-

HOH

21A-1438-

HOH

31A-1479-

HOH

41A-1529-

HOH

51A-1530-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG400 / PH range: 6.3-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.06→30 Å / Num. obs: 418461 / % possible obs: 99.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 16.66 Å2 / Rmerge(I) obs: 0.077 / Net I/av σ(I): 25.225 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.06-1.18.30.42199.9
1.1-1.147.50.288199.9
1.14-1.199.20.2351100
1.19-1.269.90.2061100
1.26-1.3412.60.1881100
1.34-1.4412.50.1431100
1.44-1.5811.50.1021100
1.58-1.8113.30.081100
1.81-2.2813.20.0651100
2.28-307.90.052196.9

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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: 1.06→29.691 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.18
RfactorNum. reflection% reflection
Rfree0.1327 20694 5.04 %
Rwork0.1253 --
obs0.1257 410323 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.37 Å2 / Biso mean: 20.9905 Å2 / Biso min: 11.66 Å2
Refinement stepCycle: final / Resolution: 1.06→29.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 0 848 5984
Biso mean---30.98 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075606
X-RAY DIFFRACTIONf_angle_d0.9997663
X-RAY DIFFRACTIONf_chiral_restr0.078856
X-RAY DIFFRACTIONf_plane_restr0.0071009
X-RAY DIFFRACTIONf_dihedral_angle_d13.7662028
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 (%)
1.0566-1.06860.16544240.15369095951968
1.0686-1.08120.16245480.144115971214587
1.0812-1.09440.17455870.151121501273791
1.0944-1.10820.15576660.1487124361310294
1.1082-1.12280.15426430.1427126201326395
1.1228-1.13820.15087550.1401129681372398
1.1382-1.15450.14717190.13611313313852100
1.1545-1.17170.14197300.13921320713937100
1.1717-1.190.15817270.13491322813955100
1.19-1.20950.15477350.13561321113946100
1.2095-1.23040.14046980.12711324413942100
1.2304-1.25270.14457150.12471323413949100
1.2527-1.27680.12947780.11781319413972100
1.2768-1.30290.12587130.11031333414047100
1.3029-1.33120.12766860.11361322913915100
1.3312-1.36220.12996930.11231329513988100
1.3622-1.39630.12266730.11061332513998100
1.3963-1.4340.12036790.10581334914028100
1.434-1.47620.10886720.10131339114063100
1.4762-1.52380.1146680.10071333714005100
1.5238-1.57830.11466200.09891338414004100
1.5783-1.64150.11337110.10141328213993100
1.6415-1.71620.11366800.10521335814038100
1.7162-1.80670.11467200.10921335814078100
1.8067-1.91980.11737360.11181335414090100
1.9198-2.0680.12757270.11151340114128100
2.068-2.27610.12817470.1131337114118100
2.2761-2.60530.1277500.12021346014210100
2.6053-3.28170.14587840.1426133391412399
3.2817-29.7030.1437100.1463127451345592

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