[English] 日本語
Yorodumi
- PDB-6tj8: Escherichia coli transketolase in complex with cofactor analog 2'... -

+
Open data


ID or keywords:

Loading...

-
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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more