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- PDB-1ngs: COMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEP... -

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Basic information

Entry
Database: PDB / ID: 1ngs
TitleCOMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEPTOR SUBSTRATE ERYTHROSE-4-PHOSPHATE
ComponentsTRANSKETOLASE
KeywordsTRANSFERASE / THIAMINE PYROPHOSPHATE / MAGNESIUM / MULTIGENE FAMILY
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase binding site / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase binding site / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / 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
ERYTHOSE-4-PHOSPHATE / THIAMINE DIPHOSPHATE / Transketolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsNilsson, U. / Lindqvist, Y. / Schneider, G.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Examination of substrate binding in thiamin diphosphate-dependent transketolase by protein crystallography and site-directed mutagenesis.
Authors: Nilsson, U. / Meshalkina, L. / Lindqvist, Y. / Schneider, G.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 A Resolution
Authors: Nikkola, M. / Lindqvist, Y. / Schneider, G.
#2: Journal: Embo J. / Year: 1992
Title: Three-Dimensional Structure of Transketolase, a Thiamine Diphosphate Dependent Enzyme, at 2.5 A Resolution
Authors: Lindqvist, Y. / Schneider, G. / Ermler, U. / Sundstrom, M.
History
DepositionSep 25, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_asym_id / _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_asym_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
B: TRANSKETOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1068
Polymers147,7752
Non-polymers1,3316
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-76 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.500, 113.300, 160.900
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: (-0.788, -0.0005, -0.6156), (0.0014, -1, -0.0011), (-0.6156, -0.0018, 0.788)
Vector: 24.8044, 132.4615, 8.6428)

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Components

#1: Protein TRANSKETOLASE /


Mass: 73887.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PTKL1 / Gene (production host): TKL1 / Production host: 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: Sugar ChemComp-E4P / ERYTHOSE-4-PHOSPHATE / Erythrose 4-phosphate


Type: saccharideCarbohydrate / Mass: 200.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9O7P
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growpH: 7.6 / Details: SEE THE PAPER, pH 7.6
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Schneider, G., (1989) J. Biol. Chem., 264, 21619.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-16 %(w/w)PEG60001drop
250 mMglycyl-glycine1drop
320 mg/mlprotein1drop
413-16 %(w/w)PEG60001reservoir
550 mMglycyl-glycine1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 45990 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 156468
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
MSCdata scaling
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 -7 %
Rwork0.206 --
obs0.206 45990 -
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10396 0 78 454 10928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.812
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.812
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: TWO-FOLD
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.251
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.812

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