[English] 日本語
Yorodumi
- PDB-1s0j: Trypanosoma cruzi trans-sialidase in complex with MuNANA (Michael... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s0j
TitleTrypanosoma cruzi trans-sialidase in complex with MuNANA (Michaelis complex)
Componentstrans-sialidase
KeywordsHYDROLASE / transglycosidase / Michaelis complex / Trypanosoma cruzi
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MUS / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAmaya, M.F. / Watts, A.G. / Damager, I. / Wehenkel, A. / Nguyen, T. / Buschiazzo, A. / Paris, G. / Frasch, A.C. / Withers, S.G. / Alzari, P.M.
Citation
Journal: Structure / Year: 2004
Title: Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase.
Authors: Amaya, M.F. / Watts, A.G. / Damager, I. / Wehenkel, A. / Nguyen, T. / Buschiazzo, A. / Paris, G. / Frasch, A.C. / Withers, S.G. / Alzari, P.M.
#1: Journal: Mol.Cell / Year: 2002
Title: The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis
Authors: Buschiazzo, A. / Amaya, M.F. / Cremona, M.L. / Frasch, A.C. / Alzari, P.M.
History
DepositionDec 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AUTHOR INDICATES THAT THE SEQUENCE IN THE DATABASE IS INCORRECT

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8132
Polymers71,3451
Non-polymers4671
Water10,359575
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.373, 129.423, 54.234
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein trans-sialidase


Mass: 71345.250 Da / Num. of mol.: 1 / Mutation: N58F,D59A,S495K,V496G,E520K,D593G,I597D,H599R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10F / References: UniProt: Q26966, exo-alpha-sialidase
#2: Chemical ChemComp-MUS / 4-METHYL-2-OXO-2H-CHROMEN-7-YL 5-(ACETYLAMINO)-3,5-DIDEOXY-L-ERYTHRO-NON-2-ULOPYRANOSIDONIC ACID / METHYLUMBELLIFERYL SIALIC ACID


Mass: 467.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25NO11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Tris-HCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 78288 / Num. obs: 78288 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.208 / % possible all: 71.7

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MS1

1ms1


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.764 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19365 3897 5 %RANDOM
Rwork0.16152 ---
obs0.16313 74362 91.82 %-
all-74362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.52 Å2
2---0.72 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 33 575 5450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9446781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4093621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.32292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.5736
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.53083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76724971
X-RAY DIFFRACTIONr_scbond_it2.71931909
X-RAY DIFFRACTIONr_scangle_it4.3574.51810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 203
Rwork0.178 4463

+
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