[English] 日本語
Yorodumi
- PDB-5xu9: Crystal Structure of Transketolase in complex with TPP intermedia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xu9
TitleCrystal Structure of Transketolase in complex with TPP intermediate IX and gauche form erythrose-4-phosphate from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


purine nucleotide metabolic process / transketolase / transketolase activity / metal ion binding
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-8N9 / ERYTHOSE-4-PHOSPHATE / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.166 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Chembiochem / Year: 2018
Title: Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Ke, S.C. / Lyu, S.Y. / Hsu, L.J. / Li, Y.S. / Chen, S.C. / Wang, K.C. / Li, T.L.
History
DepositionJun 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,52211
Polymers75,0541
Non-polymers1,46710
Water13,241735
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,04422
Polymers150,1092
Non-polymers2,93520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13410 Å2
ΔGint-34 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.259, 186.041, 98.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1442-

HOH

21A-1533-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Transketolase / TK


Mass: 75054.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: Escherichia coli (E. coli) / References: UniProt: P34736, transketolase
#5: Sugar ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O7P / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 4 types, 744 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8N9 / 2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[1,2-bis(oxidanyl)ethylidene]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate / (E)-2(3-((4-amino-2-methylpyrimidin-5-yl)methyl)-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydrothiazol-5-yl)ethyl trihydrogen diphosphate


Mass: 484.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N4O9P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. obs: 307358 / % possible obs: 95.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.45

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 1.166→19.61 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.54
RfactorNum. reflection% reflection
Rfree0.1659 14987 5 %
Rwork0.1462 --
obs0.1472 299493 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.166→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 92 735 5957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135434
X-RAY DIFFRACTIONf_angle_d1.5057388
X-RAY DIFFRACTIONf_dihedral_angle_d4.0833096
X-RAY DIFFRACTIONf_chiral_restr0.16822
X-RAY DIFFRACTIONf_plane_restr0.01954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.166-1.17930.22864220.20898956X-RAY DIFFRACTION90
1.1793-1.19310.2264450.20428923X-RAY DIFFRACTION90
1.1931-1.20770.23784310.20728976X-RAY DIFFRACTION91
1.2077-1.2230.23754850.19968953X-RAY DIFFRACTION91
1.223-1.2390.21315030.18598987X-RAY DIFFRACTION91
1.239-1.2560.19955130.18559053X-RAY DIFFRACTION92
1.256-1.2740.20954880.17879091X-RAY DIFFRACTION92
1.274-1.2930.19075010.17929122X-RAY DIFFRACTION92
1.293-1.31320.2045400.17199092X-RAY DIFFRACTION93
1.3132-1.33470.18324930.1649235X-RAY DIFFRACTION93
1.3347-1.35770.17375220.16099224X-RAY DIFFRACTION94
1.3577-1.38240.18264790.15919268X-RAY DIFFRACTION94
1.3824-1.4090.19625200.15459390X-RAY DIFFRACTION95
1.409-1.43770.17945200.15229373X-RAY DIFFRACTION95
1.4377-1.4690.17224770.13869557X-RAY DIFFRACTION96
1.469-1.50310.15644600.13499698X-RAY DIFFRACTION97
1.5031-1.54070.14645430.11629841X-RAY DIFFRACTION100
1.5407-1.58230.13955330.11249887X-RAY DIFFRACTION100
1.5823-1.62890.13975490.11349894X-RAY DIFFRACTION100
1.6289-1.68140.14335360.11659926X-RAY DIFFRACTION100
1.6814-1.74150.13595390.11659890X-RAY DIFFRACTION100
1.7415-1.81120.15145300.11999920X-RAY DIFFRACTION100
1.8112-1.89350.15295350.12529903X-RAY DIFFRACTION100
1.8935-1.99330.15934890.13159993X-RAY DIFFRACTION100
1.9933-2.1180.14644760.13259993X-RAY DIFFRACTION99
2.118-2.28130.15785470.13499810X-RAY DIFFRACTION99
2.2813-2.51050.17485070.14279797X-RAY DIFFRACTION98
2.5105-2.87280.16784400.1579686X-RAY DIFFRACTION96
2.8728-3.61570.17114660.16069794X-RAY DIFFRACTION96
3.6157-19.61240.17114980.15799274X-RAY DIFFRACTION90

+
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://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