[English] 日本語
Yorodumi
- PDB-4fpg: Crystal structure of the NanB sialidase from streptococcus pneumo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fpg
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-Hydroxybenzyl)ammonio]ethanesulfonate
ComponentsSialidase B
KeywordsHYDROLASE/INHIBITOR / hydrolase / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
BNR repeat / BNR/Asp-box repeat / 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 ...BNR repeat / BNR/Asp-box repeat / 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
2-[(3-hydroxybenzyl)amino]ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.576 Å
AuthorsBrear, P.
CitationJournal: Chembiochem / Year: 2012
Title: Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases.
Authors: Brear, P. / Telford, J. / Taylor, G.L. / Westwood, N.J.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0903
Polymers77,7811
Non-polymers3092
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.366, 82.514, 115.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sialidase B / Neuraminidase B


Mass: 77780.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-IH9 / 2-[(3-hydroxybenzyl)amino]ethanesulfonic acid


Mass: 231.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO4S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7% PEG 8000, 0.1M IMIDAZOLE, pH 8.0, vapor diffusion, sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. obs: 23163 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.104 / Χ2: 3.511 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.57-2.613.90.27911452.573198.4
2.61-2.6640.26411342.588196.5
2.66-2.713.90.2511462.684198.6
2.71-2.773.90.23611342.784197.3
2.77-2.833.80.21111532.764197.6
2.83-2.893.80.19811402.845197.6
2.89-2.973.80.18411453.102197.4
2.97-3.053.80.15711543.282197.3
3.05-3.143.90.14911173.356197.1
3.14-3.243.80.13311493.73197.1
3.24-3.353.80.1211493.826197.2
3.35-3.493.80.10811474.052197
3.49-3.653.80.111574.116197
3.65-3.843.80.09111614.258197.3
3.84-4.083.70.08411614.303197.9
4.08-4.393.60.07811384.502195.7
4.39-4.833.60.07211334.49193.7
4.83-5.5340.07212004.035197.9
5.53-6.954.30.07512333.607199.6
6.95-303.90.05912673.517196.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.23 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.58 Å27.1 Å
Translation2.58 Å27.1 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.576→27.101 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 1167 5.05 %RANDOM
Rwork0.2092 ---
obs0.2129 23110 97.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.233 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 78.96 Å2 / Biso mean: 28.1459 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--6.4996 Å2-0 Å20 Å2
2---10.8785 Å2-0 Å2
3---17.3782 Å2
Refinement stepCycle: LAST / Resolution: 2.576→27.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 19 212 5420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075328
X-RAY DIFFRACTIONf_angle_d1.1267208
X-RAY DIFFRACTIONf_chiral_restr0.075784
X-RAY DIFFRACTIONf_plane_restr0.004931
X-RAY DIFFRACTIONf_dihedral_angle_d14.2181960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.576-2.69360.35271540.2552677283197
2.6936-2.83540.30071420.21662720286298
2.8354-3.01290.30811560.20452684284098
3.0129-3.24510.34511490.21232706285597
3.2451-3.57110.28311430.20342728287197
3.5711-4.08630.26311460.19852749289597
4.0863-5.14250.21181250.18142738286395
5.1425-27.1010.29021520.23822941309399

+
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