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- PDB-4kxy: Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihy... -

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Basic information

Entry
Database: PDB / ID: 4kxy
TitleHuman transketolase in complex with ThDP analogue (R)-2-(1,2-dihydroxyethyl)-3-deaza-ThDP
ComponentsTransketolase
KeywordsTRANSFERASE / thiamin diphosphate / enzyme catalysis / pentose phosphate pathway
Function / homology
Function and homology information


D-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 / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / glyceraldehyde-3-phosphate biosynthetic process / regulation of growth ...D-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 / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / glyceraldehyde-3-phosphate biosynthetic process / 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
Chem-1U0 / Transketolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.26 Å
AuthorsNeumann, P. / Luedtke, S. / Erixon, K.M. / Leeper, F. / Kluger, R. / 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 / Category: reflns / reflns_shell / Item: _reflns.pdbx_Rsym_value
Revision 1.4Sep 20, 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 / struct_ref_seq_dif / struct_site
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_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _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)142,25637
Polymers139,2952
Non-polymers2,96135
Water26,3381462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13090 Å2
ΔGint-9 kcal/mol
Surface area39650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.150, 86.050, 92.730
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transketolase / TK


Mass: 69647.461 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 1497 molecules

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


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-1U0 / 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate


Mass: 483.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N3O9P2S
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1462 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 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 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 1.26→30 Å / Num. all: 307778 / Num. obs: 307778 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.88 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.26-1.360.5992.2519397462957199.7
1.36-1.460.4063.314589946866199.8
1.46-1.660.2096.2619868863194199.8
1.66-2.760.05319.03334550105309199.6
2.76-3.310.02138.933963412390199.5
3.31-3.860.01748.84200656292199.2
3.86-4.410.01551.7112813530198.9
4.41-140.01449.51223267026198.3
14-170.01438.86300104195.4
17-500.01534.14277110180.3

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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: 1.26→30 Å / Num. parameters: 105540 / Num. restraintsaints: 114390 / Occupancy max: 1.64 / Occupancy min: 0.03 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 17424 5 %RANDOM
Rwork0.1538 ---
all0.1651 307778 --
obs0.1538 307778 99.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 159.88 Å2 / Biso mean: 16.4439 Å2 / Biso min: -0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.26→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9494 0 182 1462 11138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d318
X-RAY DIFFRACTIONs_similar_dist67
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol51
X-RAY DIFFRACTIONs_non_zero_chiral_vol4
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.058
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.011
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0.159

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