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- PDB-5xtx: Crystal Structure of Transketolase in complex with TPP intermedia... -

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Basic information

Entry
Database: PDB / ID: 5xtx
TitleCrystal Structure of Transketolase in complex with TPP intermediate VII 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
Chem-8ML / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.049 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Chembiochem / Year: 2018
Title: Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Ke, S.C. / Lyu, S.Y. / Hsu, L.J. / Li, Y.S. / Chen, S.C. / Wang, K.C. / Li, T.L.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)76,0996
Polymers75,0541
Non-polymers1,0455
Water14,502805
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,19912
Polymers150,1092
Non-polymers2,09010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12730 Å2
ΔGint-72 kcal/mol
Surface area40920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.201, 185.345, 98.957
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-814-

HOH

21A-1161-

HOH

31A-1456-

HOH

41A-1591-

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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8ML / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2S,3S,4R,5R)-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate


Mass: 686.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33N4O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.65 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.049→30 Å / Num. obs: 425007 / % possible obs: 99.4 % / Redundancy: 6.1 % / Net I/σ(I): 35.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 1.049→23.902 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.09
RfactorNum. reflection% reflection
Rfree0.139 21459 5.05 %
Rwork0.13 --
obs0.1305 425007 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.049→23.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 64 805 5999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145481
X-RAY DIFFRACTIONf_angle_d1.4537485
X-RAY DIFFRACTIONf_dihedral_angle_d5.8583162
X-RAY DIFFRACTIONf_chiral_restr0.398840
X-RAY DIFFRACTIONf_plane_restr0.01971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.049-1.06090.1756090.152512658X-RAY DIFFRACTION93
1.0609-1.07340.15437050.137613139X-RAY DIFFRACTION97
1.0734-1.08650.14867370.13113370X-RAY DIFFRACTION99
1.0865-1.10020.13317090.124113528X-RAY DIFFRACTION100
1.1002-1.11470.13686870.117613451X-RAY DIFFRACTION100
1.1147-1.130.12646810.111913582X-RAY DIFFRACTION100
1.13-1.14610.1277820.108513387X-RAY DIFFRACTION100
1.1461-1.16320.1187400.104413548X-RAY DIFFRACTION100
1.1632-1.18140.12217540.103213476X-RAY DIFFRACTION100
1.1814-1.20080.12527470.104113495X-RAY DIFFRACTION100
1.2008-1.22150.1257660.103813483X-RAY DIFFRACTION100
1.2215-1.24370.12187380.102613496X-RAY DIFFRACTION100
1.2437-1.26760.12267450.101213538X-RAY DIFFRACTION100
1.2676-1.29350.11367040.102113482X-RAY DIFFRACTION100
1.2935-1.32160.12117190.101213586X-RAY DIFFRACTION100
1.3216-1.35240.11777290.100913566X-RAY DIFFRACTION100
1.3524-1.38620.11337080.100113541X-RAY DIFFRACTION100
1.3862-1.42370.11636640.113594X-RAY DIFFRACTION100
1.4237-1.46550.11327200.098113597X-RAY DIFFRACTION100
1.4655-1.51280.11086860.097313594X-RAY DIFFRACTION100
1.5128-1.56690.11336460.09713640X-RAY DIFFRACTION100
1.5669-1.62960.127410.102213585X-RAY DIFFRACTION100
1.6296-1.70380.12177750.109513567X-RAY DIFFRACTION100
1.7038-1.79360.12677300.115313607X-RAY DIFFRACTION100
1.7936-1.90590.14177170.124213614X-RAY DIFFRACTION100
1.9059-2.0530.13487180.125213634X-RAY DIFFRACTION100
2.053-2.25940.13296960.12713762X-RAY DIFFRACTION100
2.2594-2.5860.13357410.13613692X-RAY DIFFRACTION100
2.586-3.25680.15697310.1513522X-RAY DIFFRACTION98
3.2568-23.90840.15696340.150611814X-RAY DIFFRACTION84

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