[English] 日本語
Yorodumi
- PDB-6r8h: Triosephosphate isomerase from liver fluke (Fasciola hepatica). -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r8h
TitleTriosephosphate isomerase from liver fluke (Fasciola hepatica).
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triose Phosphate Isomerase / Fasciola Hepatica / TIM
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesFasciola hepatica (liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFerraro, F. / Corvo, I. / Bergalli, L. / Ilarraz, A. / Cabrera, M. / Gil, J. / Susuki, B. / Caffrey, C. / Timson, D.J. / Robert, X. ...Ferraro, F. / Corvo, I. / Bergalli, L. / Ilarraz, A. / Cabrera, M. / Gil, J. / Susuki, B. / Caffrey, C. / Timson, D.J. / Robert, X. / Guillon, C. / Alvarez, G.
Funding supportUruguay, 1items
OrganizationGrant numberCountry
Agencia Nacional de Investigacion e InnovacionANII-PR-UK-ID-2015-1-6Uruguay
CitationJournal: Sci Rep / Year: 2020
Title: Novel and selective inactivators of Triosephosphate isomerase with anti-trematode activity.
Authors: Ferraro, F. / Corvo, I. / Bergalli, L. / Ilarraz, A. / Cabrera, M. / Gil, J. / Susuki, B.M. / Caffrey, C.R. / Timson, D.J. / Robert, X. / Guillon, C. / Freire, T. / Alvarez, G.
History
DepositionApr 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: 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_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase
E: Triosephosphate isomerase
F: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,44712
Polymers164,8706
Non-polymers5766
Water20,1051116
1
A: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1494
Polymers54,9572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-62 kcal/mol
Surface area19730 Å2
MethodPISA
2
B: Triosephosphate isomerase
C: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1494
Polymers54,9572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-61 kcal/mol
Surface area19770 Å2
MethodPISA
3
E: Triosephosphate isomerase
F: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1494
Polymers54,9572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-62 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.420, 87.420, 186.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Triosephosphate isomerase


Mass: 27478.363 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fasciola hepatica (liver fluke) / Production host: Escherichia coli (E. coli) / References: UniProt: S4UI50, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.41 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: ZnSO4 0.01mM, MES 0.1M pH 6.5, PEG 550mme 25%w:v

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 107970 / % possible obs: 90.34 % / Redundancy: 5.15 % / Rrim(I) all: 0.144 / Net I/σ(I): 5.11
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 3604 / CC1/2: 0.729

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P61

4p61


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.81 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 5584 4.9 %RANDOM
Rwork0.1941 ---
obs0.1956 107970 90.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.39 Å2 / Biso mean: 18.12 Å2 / Biso min: 0.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11568 0 30 1116 12714
Biso mean--23.28 21.76 -
Num. residues----1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01211854
X-RAY DIFFRACTIONr_angle_refined_deg1.911.62716015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20951500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75422.884593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.156152084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2241568
X-RAY DIFFRACTIONr_chiral_restr0.1270.21515
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028974
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 168 -
Rwork0.201 3604 -
all-3772 -
obs--40.66 %

+
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