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- PDB-1gpu: Transketolase complex with reaction intermediate -

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Basic information

Entry
Database: PDB / ID: 1gpu
TitleTransketolase complex with reaction intermediate
ComponentsTRANSKETOLASE 1
KeywordsTRANSFERASE / TRANSFERASE(KETONE RESIDUES)
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytoplasm / 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-THD / Transketolase 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsFiedler, E. / Thorell, S. / Sandalova, T. / Koenig, S. / Schneider, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Snapshot of a Key Intermediate in Enzymatic Thiamin Catalysis: Crystal Structure of the Alpha-Carbanion of (Alpha,Beta-Dihydroxyethyl)-Thiamin Diphosphate in the Active Site of Transketolase ...Title: Snapshot of a Key Intermediate in Enzymatic Thiamin Catalysis: Crystal Structure of the Alpha-Carbanion of (Alpha,Beta-Dihydroxyethyl)-Thiamin Diphosphate in the Active Site of Transketolase from Saccharomyces Cerevisiae.
Authors: Fiedler, E. / Thorell, S. / Sandalova, T. / Golbik, R. / Koenig, S. / Schneider, G.
#1: Journal: Biochemistry / Year: 1997
Title: Identification of Catalytically Important Residues in Yeast Transketolase.
Authors: Wikner, C. / Nilsson, U. / Meshalkina, L. / Udekwu, C. / Lindqvist, Y. / Schneider, G.
#2: Journal: Eur.J.Biochem. / Year: 1997
Title: Examination of the Thiamin Diphosphate Binding Site in Yeasttransketolase by Site-Directed Mutagenesis
Authors: Meshalkina, L. / Nilsson, U. / Wikner, C. / Kostikowa, T.
#3: Journal: Science / Year: 1997
Title: How Thiamin Diphosphateis Activated in Enzyme
Authors: Kern, D. / Kern, G. / Neef, H. / Tittmann, K. / Killenberg-Jabs, M. / Wikner, C. / Schneider, G.
#4: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 Angstroms Resolution
Authors: Nikkola, M. / Lindqvist, Y. / Schneider, G.
History
DepositionNov 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2002Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSKETOLASE 1
B: TRANSKETOLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8246
Polymers147,7752
Non-polymers1,0494
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-77.1 kcal/mol
Surface area41570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.300, 113.200, 159.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.787981, 0.002369, -0.615696), (0.001263, -0.999984, -0.005464), (-0.615699, -0.005083, 0.787965)
Vector: 24.515, 133.213, 8.815)

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Components

#1: Protein TRANSKETOLASE 1 / TK 1


Mass: 73887.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P23254, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THD / 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE / ({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE


Mass: 484.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N4O9P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.27 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.9 / Details: pH 7.90
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-17 %(w/v)PEG60001reservoir
25 mMThDP1reservoir
35 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459
DetectorDate: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 104364 / % possible obs: 92.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.9
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.5 / % possible all: 89
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 333802

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRK

1trk


Resolution: 1.86→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 -7.2 %RANDOM
Rwork0.198 ---
obs0.198 104364 92.8 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 59.9 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--11 Å20 Å20 Å2
2--5.83 Å20 Å2
3---5.17 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10394 0 62 859 11315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005653
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.27876
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.86→1.87 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.2909 103
Rwork0.2675 1562
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TPI.PARTPI.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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