[English] 日本語
Yorodumi
- PDB-1sux: CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sux
TitleCRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI AND 3-(2-benzothiazolylthio)-1-propanesulfonic acid
ComponentsTriosephosphate isomerase, glycosomal
KeywordsISOMERASE / TRIOSEPHOSPHATE ISOMERASE / TRYPANOSOMA CRUZI / PROTEIN INTERFACES / BENZOTHIAZOLE INHIBITOR
Function / homology
Function and homology information


glycosome / 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
3-(2-BENZOTHIAZOLYLTHIO)-1-PROPANESULFONIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTellez-Valencia, A. / Olivares-Illana, V. / Hernandez-Santoyo, A. / Perez-Montfort, R. / Costas, M. / Rodriguez-Romero, A. / Tuena De Gomez-Puyou, M. / Gomez-Puyou, A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Inactivation of triosephosphate isomerase from Trypanosoma cruzi by an agent that perturbs its dimer interface.
Authors: Tellez-Valencia, A. / Olivares-Illana, V. / Hernandez-Santoyo, A. / Perez-Montfort, R. / Costas, M. / Rodriguez-Romero, A. / Lopez-Calahorra, F. / Tuena De Gomez-Puyou, M. / Gomez-Puyou, A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Differences in the intersubunit contacts in triosephosphate isomerase from two closely related pathogenic trypanosomes
Authors: Maldonado, E. / Soriano-Garcia, M. / Moreno, A. / Cabrera, N. / Garza-Ramos, G. / De Gomez-Puyou, M. / Gomez-Puyou, A. / Perez-Montfort, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane
Authors: Gao, X.G. / Maldonado, E. / Perez-Monfort, R. / Garza-Ramos, G. / De Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, A.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate isomerase, glycosomal
B: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,68310
Polymers54,7212
Non-polymers9628
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-104 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.870, 75.580, 146.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Triosephosphate isomerase, glycosomal / / TIM


Mass: 27360.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: MEXICAN NINOA STRAIN / Plasmid: PET23A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3) / References: UniProt: P52270, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTS / 3-(2-BENZOTHIAZOLYLTHIO)-1-PROPANESULFONIC ACID


Mass: 289.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO3S3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, HEPES, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 21, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 31622 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.04

-
Processing

Software
NameVersionClassification
CNS1.1refinement
bioteXdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCD

1tcd


Resolution: 2→23.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1724206.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FIVE DISCRETELY DISORDERED RESIDUES: GLU 19, GLU 27, LYS 53, SER 97 OF MONOMER A AND SER 2 0F MONOMER B. RESIDUE MET 1 OF BOTH CHAINS AND SIDE CHAINS FROM CG OF RESIDUES LYS A 157, LYS A ...Details: FIVE DISCRETELY DISORDERED RESIDUES: GLU 19, GLU 27, LYS 53, SER 97 OF MONOMER A AND SER 2 0F MONOMER B. RESIDUE MET 1 OF BOTH CHAINS AND SIDE CHAINS FROM CG OF RESIDUES LYS A 157, LYS A 177, GLN A 182 AND LYS B 218 HAVE WEAK ELECTRON DENSITY AND ARE NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2927 10 %RANDOM
Rwork0.183 ---
obs0.183 29330 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7691 Å2 / ksol: 0.402909 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--0.43 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 2→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 52 374 4257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.191 365 9.9 %
Rwork0.177 3325 -
obs-3325 68.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SO4_XPLOR_PAR.PARAMSO4_XPLOR_PAR.TOP
X-RAY DIFFRACTION3BTS_PARB.PARAMBTS_PARB.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP

+
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