[English] 日本語
Yorodumi
- PDB-9db6: Sialidase682 co-crystallized with inhibitor DANA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9db6
TitleSialidase682 co-crystallized with inhibitor DANA
ComponentsBNR/Asp-box repeat protein
KeywordsHYDROLASE / Sialidase / sialic acid inhibitor complex
Function / homology2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / :
Function and homology information
Biological speciesBacteroides finegoldii DSM 17565 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYoung, M.A. / Rees, S.D. / Chang, G.
Funding support1items
OrganizationGrant numberCountry
Not fundedNone
CitationJournal: To Be Published
Title: Sialidase682 co-crystallized with inhibitor DANA
Authors: Young, M.A. / Rees, S.D. / Chang, G.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
C: BNR/Asp-box repeat protein
D: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,3578
Polymers242,1924
Non-polymers1,1654
Water18,7361040
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-11 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.248, 149.520, 100.437
Angle α, β, γ (deg.)90.000, 113.299, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
BNR/Asp-box repeat protein


Mass: 60547.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides finegoldii DSM 17565 (bacteria)
Gene: BACFIN_07125
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9KXU6
#2: Sugar
ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: P 1 21 1 space group
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: After 6 weeks, crystals formed on the PEGIon tray condition 0.2M sodium malonate pH 4.0, 20% w/v Polyethylene glycol 3,350 at 289.15K

-
Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.1→78.51 Å / Num. obs: 126161 / % possible obs: 99.76 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.51 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.101 / Rrim(I) all: 0.152 / Χ2: 0.47 / Net I/σ(I): 1.4
Reflection shellResolution: 2.1→7.25 Å / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 5927 / CC1/2: 0.987 / Rpim(I) all: 0.101 / Rrim(I) all: 0.152 / Χ2: 1.07 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALS2.2data reduction
Aimless0.7.4data scaling
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→78.51 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 6304 5 %
Rwork0.2072 119855 -
obs0.2087 126159 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→78.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16340 0 80 1040 17460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716776
X-RAY DIFFRACTIONf_angle_d0.878122744
X-RAY DIFFRACTIONf_chiral_restr0.05652564
X-RAY DIFFRACTIONf_plane_restr0.0072884
X-RAY DIFFRACTIONf_dihedral_angle_d15.17926288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.44742180.36453914X-RAY DIFFRACTION98.71
2.12-2.150.3622130.35183963X-RAY DIFFRACTION98.75
2.15-2.180.36551850.35383981X-RAY DIFFRACTION99.31
2.18-2.20.37532040.34623957X-RAY DIFFRACTION99.14
2.2-2.230.3272050.31554013X-RAY DIFFRACTION99.67
2.23-2.260.32341770.29583980X-RAY DIFFRACTION99.71
2.26-2.290.31842040.29284002X-RAY DIFFRACTION99.72
2.29-2.330.33132300.2973909X-RAY DIFFRACTION99.4
2.33-2.370.31372150.2764018X-RAY DIFFRACTION99.79
2.37-2.40.31742060.27123990X-RAY DIFFRACTION99.74
2.4-2.450.2892040.25973991X-RAY DIFFRACTION99.9
2.45-2.490.29672010.25563970X-RAY DIFFRACTION99.88
2.49-2.540.3082140.26154015X-RAY DIFFRACTION99.93
2.54-2.590.2792310.25053982X-RAY DIFFRACTION99.88
2.59-2.650.28442130.25393983X-RAY DIFFRACTION99.9
2.65-2.710.29662180.25563955X-RAY DIFFRACTION99.9
2.71-2.780.32322050.25724025X-RAY DIFFRACTION99.98
2.78-2.850.25531990.24083978X-RAY DIFFRACTION99.95
2.85-2.930.25262420.22563987X-RAY DIFFRACTION99.98
2.93-3.030.25041890.21744023X-RAY DIFFRACTION99.98
3.03-3.140.25652270.214003X-RAY DIFFRACTION99.95
3.14-3.260.23492360.20593980X-RAY DIFFRACTION100
3.26-3.410.24282110.20323983X-RAY DIFFRACTION99.98
3.41-3.590.22282310.20154022X-RAY DIFFRACTION100
3.59-3.820.20341960.17914013X-RAY DIFFRACTION100
3.82-4.110.19542050.16574011X-RAY DIFFRACTION100
4.11-4.520.1691940.14064041X-RAY DIFFRACTION100
4.52-5.180.1582070.12674033X-RAY DIFFRACTION99.98
5.18-6.520.16121970.15534050X-RAY DIFFRACTION100
6.52-78.510.2062270.17714083X-RAY DIFFRACTION99.72

+
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