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- PDB-2r8o: Transketolase from E. coli in complex with substrate D-xylulose-5... -

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Basic information

Entry
Database: PDB / ID: 2r8o
TitleTransketolase from E. coli in complex with substrate D-xylulose-5-phosphate
ComponentsTransketolase 1
KeywordsTRANSFERASE / reaction intermediate / Calcium / Metal-binding / Thiamine pyrophosphate
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity / 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, C-terminal domain ...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-T5X / Transketolase 1
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsWille, G. / Asztalos, P. / Weiss, M.S. / Tittmann, K.
CitationJournal: Biochemistry / Year: 2007
Title: Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and ...Title: Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate.
Authors: Asztalos, P. / Parthier, C. / Golbik, R. / Kleinschmidt, M. / Hubner, G. / Weiss, M.S. / Friedemann, R. / Wille, G. / Tittmann, K.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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_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)148,31717
Polymers146,2432
Non-polymers2,07415
Water21,6541202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.138, 101.951, 133.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transketolase 1 / TK 1


Mass: 73121.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: tktA, tkt / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P27302, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-T5X / 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol / D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT


Mass: 655.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H30N4O15P3S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1202 / 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: 41.24 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 6000, glycerol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.47→27.4 Å / Num. all: 208542 / Num. obs: 207914 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.981 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.47-1.4910.60.31768430.96199.2
1.49-1.510.60.30468390.95399.3
1.5-1.5210.60.2868520.96999.4
1.52-1.5410.60.25567860.98299.3
1.54-1.5610.60.23968670.96999.6
1.56-1.5810.60.22668740.96399.7
1.58-1.6110.70.21168240.97899.6
1.61-1.6310.80.20268820.96799.8
1.63-1.6610.80.18668800.95799.9
1.66-1.6810.80.17668730.98299.9
1.68-1.7110.90.16669130.96699.9
1.71-1.7410.90.15168680.965100
1.74-1.7811.10.1468810.97100
1.78-1.8111.20.13169190.965100
1.81-1.8511.30.11969270.966100
1.85-1.911.40.10968840.984100
1.9-1.9411.50.09969260.999100
1.94-211.70.08869240.973100
2-2.0511.80.0869170.987100
2.05-2.1211.90.07469331.001100
2.12-2.211.90.06869370.981100
2.2-2.28120.06369221.003100
2.28-2.39120.05869650.987100
2.39-2.51120.05469810.988100
2.51-2.67120.05169690.999100
2.67-2.88120.04869770.998100
2.88-3.17120.04470320.999100
3.17-3.63120.03970380.998100
3.63-4.5711.90.03571401.003100
4.57-9911.50.03573410.99899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→27.14 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.782 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 2094 1 %RANDOM
Rwork0.15 ---
all0.15 208119 --
obs0.15 207809 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10254 0 126 1202 11582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210622
X-RAY DIFFRACTIONr_angle_refined_deg1.281.97514406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62251351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16624.289478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.153151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3181556
X-RAY DIFFRACTIONr_chiral_restr0.0820.21537
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028136
X-RAY DIFFRACTIONr_nbd_refined0.190.25285
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.21022
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.238
X-RAY DIFFRACTIONr_mcbond_it0.5341.56804
X-RAY DIFFRACTIONr_mcangle_it0.825210558
X-RAY DIFFRACTIONr_scbond_it1.55334367
X-RAY DIFFRACTIONr_scangle_it2.3764.53836
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 152 -
Rwork0.146 14962 -
all-15114 -
obs--99.27 %

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