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- PDB-6tj8: Escherichia coli transketolase in complex with cofactor analog 2'... -

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Basic information

Entry
Database: PDB / ID: 6tj8
TitleEscherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine diphosphate
ComponentsTransketolase 1
KeywordsTRANSFERASE / THIAMIN DIPHOSPHATE / ENZYME CATALYSIS / PENTOSE PHOSPHATE PATHWAY
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-NDQ / Transketolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.921 Å
AuthorsRabe von Pappenheim, F. / Tittmann, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR 1296/TP3 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine.
Authors: Rabe von Pappenheim, F. / Aldeghi, M. / Shome, B. / Begley, T. / de Groot, B.L. / Tittmann, K.
History
DepositionNov 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: 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 1
B: Transketolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,25439
Polymers146,2432
Non-polymers3,01137
Water28,6261589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint55 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.550, 101.910, 132.960
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 (strain K12) (bacteria)
Strain: K12 / Gene: tktA, tkt, b2935, JW5478 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27302, transketolase
#2: Chemical ChemComp-NDQ / 2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 441.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1589 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: PEG6000, Glycerol, Glycyl-Glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.92→47.3 Å / Num. obs: 780617 / % possible obs: 93.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 7.62 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.095 / Net I/σ(I): 9.73
Reflection shellResolution: 0.92→0.95 Å / Redundancy: 2.9 % / Num. unique obs: 46733 / CC1/2: 0.67 / Rrim(I) all: 0.061 / % possible all: 61.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata processing
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGD

1qgd


Resolution: 0.921→47.285 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 8.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1064 23418 3 %
Rwork0.0948 757181 -
obs0.0952 780599 94.19 %
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.08 Å2 / Biso mean: 10.5689 Å2 / Biso min: 2.75 Å2
Refinement stepCycle: final / Resolution: 0.921→47.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10219 0 528 1638 12385
Biso mean--14.78 23.2 -
Num. residues----1331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.9212-0.93160.25063140.22121015338
0.9316-0.94260.2136470.20422091478
0.9426-0.95410.21346850.192213883
0.9541-0.96620.19437380.18112386790
0.9662-0.97890.18787520.16782431191
0.9789-0.99230.16997580.15452452392
0.9923-1.00650.14667690.14192485393
1.0065-1.02150.14517830.13282531195
1.0215-1.03750.13827900.1192559596
1.0375-1.05450.12768000.10652585897
1.0545-1.07260.11188000.09322587397
1.0726-1.09220.09888050.08532602097
1.0922-1.11320.08978040.07872598998
1.1132-1.13590.08868070.07552611398
1.1359-1.16060.08968070.07082608498
1.1606-1.18760.08188060.06912606297
1.1876-1.21730.08158120.06682625298
1.2173-1.25020.08158140.06642632899
1.2502-1.2870.08368160.06742637099
1.287-1.32850.08348170.0682643599
1.3285-1.3760.08298190.06782646599
1.376-1.43110.08658190.06652647899
1.4311-1.49630.07978190.06672649399
1.4963-1.57510.07788250.06692665199
1.5751-1.67380.08088270.07092675899
1.6738-1.80310.08458280.07962677599
1.8031-1.98450.09128290.08522681499
1.9845-2.27170.0998340.087826952100
2.2717-2.8620.1088390.102227134100
2.862-47.2850.13548550.12472761299

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