[English] 日本語
Yorodumi
- PDB-9hbe: The RSL - phosphonato-calix[6]arene cocrystal structure, pH 8.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hbe
TitleThe RSL - phosphonato-calix[6]arene cocrystal structure, pH 8.5
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / lectin / trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / phosphonato-calix[6]arene / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsMockler, N.M. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Irish Research CouncilGOIPG/2021/333 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Chemistry / Year: 2025
Title: Making and Breaking Supramolecular Synthons for Modular Protein Frameworks.
Authors: Mockler, N.M. / Raston, C.L. / Crowley, P.B.
History
DepositionNov 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,83812
Polymers19,4672
Non-polymers5,37110
Water4,900272
1
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4196
Polymers9,7341
Non-polymers2,6865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4196
Polymers9,7341
Non-polymers2,6865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.149, 83.149, 157.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-319-

HOH

31B-321-

HOH

41B-399-

HOH

51B-418-

HOH

-
Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9733.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-7AZ / phosphonato-calix[6]arene


Mass: 1116.611 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H42O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26 M Ammonium sulfate, 0.1 M TRIS pH 8.5, 0.2 M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.19→53.19 Å / Num. obs: 67645 / % possible obs: 99.9 % / Redundancy: 17.1 % / Biso Wilson estimate: 14.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.5
Reflection shellResolution: 1.19→1.21 Å / Num. unique obs: 3253 / CC1/2: 0.532 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→53.19 Å / SU ML: 0.1377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 3396 5.07 %
Rwork0.1765 63565 -
obs0.1774 66961 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.04 Å2
Refinement stepCycle: LAST / Resolution: 1.19→53.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 348 272 1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411786
X-RAY DIFFRACTIONf_angle_d0.81722532
X-RAY DIFFRACTIONf_chiral_restr0.0769228
X-RAY DIFFRACTIONf_plane_restr0.0059264
X-RAY DIFFRACTIONf_dihedral_angle_d9.9828696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20.33361230.35022198X-RAY DIFFRACTION82.01
1.2-1.220.38621170.32932421X-RAY DIFFRACTION92.02
1.22-1.240.30521340.30422662X-RAY DIFFRACTION99.64
1.24-1.260.30161340.29522620X-RAY DIFFRACTION99.89
1.26-1.280.30181410.27282682X-RAY DIFFRACTION100
1.28-1.310.30221360.26352650X-RAY DIFFRACTION100
1.31-1.330.28441280.24892664X-RAY DIFFRACTION99.79
1.33-1.360.25391580.23642642X-RAY DIFFRACTION99.96
1.36-1.390.23381470.21922657X-RAY DIFFRACTION99.96
1.39-1.420.25441380.21292674X-RAY DIFFRACTION100
1.42-1.460.21851340.20132668X-RAY DIFFRACTION99.96
1.46-1.50.25061370.19472661X-RAY DIFFRACTION100
1.5-1.540.23531410.18472674X-RAY DIFFRACTION100
1.54-1.590.19771530.18022639X-RAY DIFFRACTION100
1.59-1.650.17581440.16432680X-RAY DIFFRACTION99.93
1.65-1.710.18971270.17262696X-RAY DIFFRACTION100
1.71-1.790.18051540.17232655X-RAY DIFFRACTION100
1.79-1.890.21390.17712700X-RAY DIFFRACTION99.96
1.89-20.17631450.16562677X-RAY DIFFRACTION99.96
2-2.160.18871710.17392659X-RAY DIFFRACTION99.86
2.16-2.380.17091520.17122718X-RAY DIFFRACTION100
2.38-2.720.21531460.17962681X-RAY DIFFRACTION100
2.72-3.430.18951490.16892757X-RAY DIFFRACTION100
3.43-53.190.1451480.13652830X-RAY DIFFRACTION99.6

+
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