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- PDB-6rjc: E.coli transketolase apoenzyme -

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Basic information

Entry
Database: PDB / ID: 6rjc
TitleE.coli transketolase apoenzyme
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 signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.05 Å
AuthorsRabe von Pappenheim, F. / Tittmann, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR 1296/TP3 Germany
CitationJournal: Nature / Year: 2019
Title: Low-barrier hydrogen bonds in enzyme cooperativity.
Authors: Dai, S. / Funk, L.M. / von Pappenheim, F.R. / Sautner, V. / Paulikat, M. / Schroder, B. / Uranga, J. / Mata, R.A. / Tittmann, K.
History
DepositionApr 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_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

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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)149,37653
Polymers146,2432
Non-polymers3,13351
Water27,9411551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18590 Å2
ΔGint67 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.905, 102.048, 132.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 1602 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1551 / 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: 41.28 %
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: 0.8266 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.05→80.95 Å / Num. obs: 549750 / % possible obs: 97.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.25 Å2 / CC1/2: 1 / Rrim(I) all: 0.055 / Net I/σ(I): 15.71
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.36 / Num. unique obs: 57085 / CC1/2: 0.685 / Rrim(I) all: 0.818 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998phasing
RefinementResolution: 1.05→80.947 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1233 16493 3 %
Rwork0.1036 --
obs0.1042 549749 97.49 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→80.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10228 0 198 1551 11977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611797
X-RAY DIFFRACTIONf_angle_d0.99116027
X-RAY DIFFRACTIONf_dihedral_angle_d15.5014477
X-RAY DIFFRACTIONf_chiral_restr0.0791663
X-RAY DIFFRACTIONf_plane_restr0.0072148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06190.23295390.213817417X-RAY DIFFRACTION96
1.0619-1.07440.21395370.197417388X-RAY DIFFRACTION96
1.0744-1.08750.2075400.186317437X-RAY DIFFRACTION96
1.0875-1.10130.18565370.172517377X-RAY DIFFRACTION96
1.1013-1.11580.18625400.160317447X-RAY DIFFRACTION96
1.1158-1.13110.17545400.148917486X-RAY DIFFRACTION96
1.1311-1.14720.16285410.142117472X-RAY DIFFRACTION96
1.1472-1.16440.16285400.135317475X-RAY DIFFRACTION96
1.1644-1.18260.15165390.128317418X-RAY DIFFRACTION96
1.1826-1.2020.13025420.11817536X-RAY DIFFRACTION97
1.202-1.22270.13415460.112417633X-RAY DIFFRACTION97
1.2227-1.24490.13075480.104817713X-RAY DIFFRACTION97
1.2449-1.26890.12855480.100117718X-RAY DIFFRACTION98
1.2689-1.29480.12395490.098817752X-RAY DIFFRACTION98
1.2948-1.32290.12195500.094417791X-RAY DIFFRACTION98
1.3229-1.35370.11275480.091117738X-RAY DIFFRACTION98
1.3537-1.38760.11355550.088917919X-RAY DIFFRACTION98
1.3876-1.42510.12475510.085317816X-RAY DIFFRACTION98
1.4251-1.4670.10415530.080617879X-RAY DIFFRACTION98
1.467-1.51440.1065530.075217890X-RAY DIFFRACTION98
1.5144-1.56850.09345500.072417796X-RAY DIFFRACTION98
1.5685-1.63130.09515500.072317788X-RAY DIFFRACTION98
1.6313-1.70550.0995570.074718002X-RAY DIFFRACTION98
1.7055-1.79550.09355580.077718040X-RAY DIFFRACTION99
1.7955-1.9080.1055600.081318111X-RAY DIFFRACTION99
1.908-2.05530.10565600.085918113X-RAY DIFFRACTION99
2.0553-2.26210.09795630.087318189X-RAY DIFFRACTION99
2.2621-2.58950.11525630.093818199X-RAY DIFFRACTION99
2.5895-3.26250.11925630.110218197X-RAY DIFFRACTION98
3.2625-81.18850.14385730.126218519X-RAY DIFFRACTION97

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