[English] 日本語
Yorodumi
- PDB-9hrx: The RSL - pctx complex, H32 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hrx
TitleThe RSL - pctx complex, H32 form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / : / ACETATE ION / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsWren, C.P. / Flood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Protein Recognition and Assembly by a Phosphocavitand.
Authors: Wren, C.P. / Flood, R.J. / Mockler, N.M. / Savko, M. / Malinska, M. / Shi, Q. / Crowley, P.B.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
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)23,49322
Polymers19,4672
Non-polymers4,02620
Water3,621201
1
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,80512
Polymers9,7341
Non-polymers2,07211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,68710
Polymers9,7341
Non-polymers1,9549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.893, 45.893, 421.816
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-109-

ZN

21B-107-

ZN

31A-211-

HOH

41A-290-

HOH

51A-301-

HOH

61A-307-

HOH

71B-278-

HOH

81B-279-

HOH

-
Components

-
Protein / Sugars , 2 types, 6 molecules AB

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


Mass: 9733.562 Da / Num. of mol.: 2 / Mutation: 0
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
#4: 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
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

-
Non-polymers , 4 types, 217 molecules

#2: Chemical
ChemComp-A1IXG / phosphated-cyclotrixylohydroquinoylene


Mass: 636.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H27O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 3350, 0.2 M zinc acetate, 0.1 M Imidazole pH 7.8

-
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: Nov 11, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.49→39.057 Å / Num. obs: 28854 / % possible obs: 99.8 % / Redundancy: 17.1 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.018 / Rrim(I) all: 0.077 / Net I/σ(I): 24.9
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 1339 / CC1/2: 0.955 / Rpim(I) all: 0.089 / Rrim(I) all: 0.321 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→37.19 Å / SU ML: 0.1488 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.0381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 1453 5.04 %
Rwork0.181 27399 -
obs0.1823 28852 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.49→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 240 201 1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371670
X-RAY DIFFRACTIONf_angle_d1.14782358
X-RAY DIFFRACTIONf_chiral_restr0.0681228
X-RAY DIFFRACTIONf_plane_restr0.0043390
X-RAY DIFFRACTIONf_dihedral_angle_d7.0023366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.550.23481480.19722597X-RAY DIFFRACTION97.62
1.55-1.610.20851300.18782696X-RAY DIFFRACTION100
1.61-1.680.19751310.18162719X-RAY DIFFRACTION100
1.68-1.770.21021440.18092717X-RAY DIFFRACTION100
1.77-1.880.23011470.19322683X-RAY DIFFRACTION100
1.88-2.030.23171370.19232743X-RAY DIFFRACTION100
2.03-2.230.22921520.18662711X-RAY DIFFRACTION100
2.23-2.550.20491250.19212807X-RAY DIFFRACTION100
2.55-3.210.22941540.18112774X-RAY DIFFRACTION100
3.22-37.190.16911850.16172952X-RAY DIFFRACTION99.94

+
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