[English] 日本語
Yorodumi
- PDB-2sli: LEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH 2,7-ANHYDRO-N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sli
TitleLEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH 2,7-ANHYDRO-NEU5AC, THE REACTION PRODUCT
ComponentsINTRAMOLECULAR TRANS-SIALIDASE
KeywordsHYDROLASE / INTRAMOLECULAR TRANS-SIALIDASE / NEURAMINIDASE
Function / homology
Function and homology information


anhydrosialidase / anhydrosialidase activity / exo-alpha-sialidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily ...Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / 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 / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SKD / Anhydrosialidase
Similarity search - Component
Biological speciesMacrobdella decora (North American leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLuo, Y. / Li, S.C. / Li, Y.T. / Luo, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The 1.8 A structures of leech intramolecular trans-sialidase complexes: evidence of its enzymatic mechanism.
Authors: Luo, Y. / Li, S.C. / Li, Y.T. / Luo, M.
History
DepositionOct 3, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTRAMOLECULAR TRANS-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8572
Polymers74,5661
Non-polymers2911
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.364, 69.275, 72.469
Angle α, β, γ (deg.)113.48, 95.41, 107.31
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein INTRAMOLECULAR TRANS-SIALIDASE


Mass: 74565.688 Da / Num. of mol.: 1 / Fragment: DEVOID OF N-TERMINAL 28 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrobdella decora (North American leech)
Gene: T7 / Plasmid: E2-M10 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q27701, exo-alpha-sialidase
#2: Chemical ChemComp-SKD / 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID / 2,7-ANHYDRO-NEU5AC


Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Luo, Y., (1998) Acta Cryst., D54, 111.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 %PEG60001reservoir
30.1 Mcacodylate1reservoir
40.25 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 24, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 63696 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.173 / % possible all: 67.6
Reflection
*PLUS
Num. measured all: 122932 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 67.6 % / Rmerge(I) obs: 0.173

-
Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE

Resolution: 1.8→15 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.224 -10 %RANDOM
Rwork0.185 ---
obs0.185 63348 90.2 %-
Displacement parametersBiso mean: 11.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 20 593 5870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROPARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOSKD.TOP
X-RAY DIFFRACTION4SKD.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_deg1.33

+
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