[English] 日本語
Yorodumi
- PDB-9sjj: Crystal structure of SusDdex (BT3089) with bound IMO5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sjj
TitleCrystal structure of SusDdex (BT3089) with bound IMO5
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / BT3089 / SusDdex / SusD / dextran / Bacteroides / glycan-binding
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFeasey, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural and functional characterisation of the dextran utilisome from Bacteroides thetaiotaomicron
Authors: Feasey, M. / Silale, A. / Basle, A. / van den Berg, B.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,26018
Polymers53,8141
Non-polymers3,44617
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-4 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87, 106.15, 138.34
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein SusD homolog


Mass: 53814.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3089
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A366
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 326 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Lithium sulfate 0.1M Sodium acetate pH 4.5 50% w/v PEG 400 Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment ...Details: 0.2M Lithium sulfate 0.1M Sodium acetate pH 4.5 50% w/v PEG 400 Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment harvested for the synchrotron.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→67.29 Å / Num. obs: 70548 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 0.99 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-67.2923.90.04470.454810.0120.0460.9799.7
1.7-1.7327.43.0151.336900.5870.8323.1290.93100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
BUSTERrefinement
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→67.288 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.813 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.082 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.191 3544 5.024 %
Rwork0.1647 67004 -
all0.166 --
obs-70548 99.991 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.001 Å2-0 Å20 Å2
2--0.457 Å2-0 Å2
3---0.545 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 224 310 4179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123938
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.8075300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.255524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77310606
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.310188
X-RAY DIFFRACTIONr_chiral_restr0.1410.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022931
X-RAY DIFFRACTIONr_nbd_refined0.210.21938
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0640.219
X-RAY DIFFRACTIONr_mcbond_it2.913.1871847
X-RAY DIFFRACTIONr_mcangle_it3.8765.7112307
X-RAY DIFFRACTIONr_scbond_it4.7883.6152091
X-RAY DIFFRACTIONr_scangle_it6.4376.4042993
X-RAY DIFFRACTIONr_lrange_it7.35434.4466192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2892530.2849360.28151890.9410.9451000.266
1.744-1.7920.2592190.2447840.2450030.9530.961000.219
1.792-1.8440.2532440.21846590.21949030.9560.9691000.192
1.844-1.9010.2192330.19445360.19547690.9690.9751000.165
1.901-1.9630.2162300.17643590.17845890.9710.981000.147
1.963-2.0320.2232450.16842420.17144880.9690.98199.97770.141
2.032-2.1080.2062220.15840890.16143110.9760.9841000.135
2.108-2.1940.1642280.14839140.14941430.9830.98799.97590.128
2.194-2.2920.1792150.14837910.1540060.9790.9871000.129
2.292-2.4030.171780.14136270.14238050.9820.9881000.123
2.403-2.5330.1651710.14634840.14736550.9830.9871000.129
2.533-2.6870.1961660.14432770.14734430.9790.9881000.131
2.687-2.8720.1791580.15831100.15932690.9790.98699.96940.148
2.872-3.1010.1831690.16728430.16830120.980.9841000.161
3.101-3.3970.21420.17526690.17728110.9770.9821000.175
3.397-3.7970.1711360.16524130.16625490.9840.9851000.172
3.797-4.3820.1541280.14121240.14122520.9880.9891000.155
4.382-5.3610.194810.14218530.14419340.9780.9891000.166
5.361-7.5570.196890.18614340.18615230.9820.9821000.212
7.557-67.2880.313370.2188600.2218970.9480.9741000.266

+
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