[English] 日本語
Yorodumi
- PDB-1sll: SIALIDASE L FROM LEECH MACROBDELLA DECORA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sll
TitleSIALIDASE L FROM LEECH MACROBDELLA DECORA
ComponentsSIALIDASE L
KeywordsHYDROLASE / SIALIDASE
Function / homology
Function and homology information


anhydrosialidase / anhydrosialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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
Biological speciesMacrobdella decora (North American leech)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsLuo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity.
Authors: Luo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M.
History
DepositionOct 14, 1997Processing site: BNL
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIALIDASE L


Theoretical massNumber of molelcules
Total (without water)74,5661
Polymers74,5661
Non-polymers00
Water12,268681
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 SIALIDASE L


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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 %
Description: HEAVY ATOM LOCATION WERE ASSISTED BY AN INCOMPLETE MOLECULAR REPLACEMENT MODEL.
Crystal growMethod: macroseeding / pH: 6.3
Details: THE PROTEIN WAS CRYSTALLIZED BY MACROSEEDING IN 20% PEG 6000, 0.25 M NACL, 0.1 M CACODYLATE BUFFER, PH 6.3., macroseeding
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlenzyme1drop
20.1 Mcacodylate1reservoir
320 %PEG60001reservoir
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: Dec 24, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 48513 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 16
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 13.5 / Rsym value: 0.088 / % possible all: 94.2
Reflection
*PLUS
Num. obs: 48481 / Num. measured all: 145108 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 94.2 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→6 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
Rwork0.167 ---
obs0.167 47213 93.4 %-
Displacement parametersBiso mean: 11.9 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 0 681 5938
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 47204 / Rfactor obs: 0.166 / Rfactor Rfree: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.64
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_deg1.27

+
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