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- PDB-4kxu: Human transketolase in covalent complex with donor ketose D-fruct... -

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Basic information

Entry
Database: PDB / ID: 4kxu
TitleHuman transketolase in covalent complex with donor ketose D-fructose-6-phosphate
ComponentsTransketolase
KeywordsTRANSFERASE / thiamin diphosphate / enzyme catalysis / pentose phosphate pathway
Function / homology
Function and homology information


xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / regulation of growth ...xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / regulation of growth / thiamine pyrophosphate binding / peroxisome / vesicle / nuclear body / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
: / Transketolase, 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, 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
D-SORBITOL-6-PHOSPHATE / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.98 Å
AuthorsNeumann, P. / Luedtke, S. / Ficner, R. / Tittmann, K.
CitationJournal: Nat Chem / Year: 2013
Title: Sub-angstrom-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate.
Authors: Ludtke, S. / Neumann, P. / Erixon, K.M. / Leeper, F. / Kluger, R. / Ficner, R. / Tittmann, K.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,06516
Polymers69,6471
Non-polymers1,41815
Water14,772820
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,13032
Polymers139,2952
Non-polymers2,83530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14450 Å2
ΔGint-10 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.760, 85.880, 72.990
Angle α, β, γ (deg.)90.00, 125.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7638-

HOH

21A-7744-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Transketolase / TK


Mass: 69647.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TKT / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29401, transketolase
#5: Sugar ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P

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Non-polymers , 5 types, 834 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsS6P A1014 IS A HYDROLYZED FRUCTOSE-6-PHOSPHATE COVALENTLY LINKED TO TDP A1015

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: Reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v), 2 % glycerol (v/v) , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93939 Å / Relative weight: 1
ReflectionResolution: 0.98→30 Å / Num. all: 300587 / Num. obs: 300587 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 9.844 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
0.98-1.050.5032.9317168047462177.8
1.05-1.180.2226.6928425572418192.4
1.18-1.20.1499.35341888657193.7
1.2-1.30.12810.6714116135833194.4
1.3-1.40.09912.9810467726611195.3
1.4-1.50.07915.17884620129195.9
1.5-1.70.06218.311106127637196.6
1.7-1.80.0622.38500209587197.3
1.8-20.05328.758833214003197.6
2-30.0446.821486726853198.4
3-100.02963.037671611131198.3
10-500.0267.761336266178.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3MOS

3mos


Resolution: 0.98→30 Å / Num. parameters: 57058 / Num. restraintsaints: 62047 / Occupancy max: 1 / Occupancy min: 0.04 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1224 3006 1 %RANDOM
Rwork0.1015 ---
all0.103 297579 --
obs0.1015 246963 91.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 184.87 Å2 / Biso mean: 13.6034 Å2 / Biso min: 2.11 Å2
Refinement stepCycle: LAST / Resolution: 0.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 88 820 5655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d305
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol75
X-RAY DIFFRACTIONs_non_zero_chiral_vol2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.109
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.014
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0.12

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