[English] 日本語
Yorodumi
- PDB-9g3r: LecA from Pseudomonas aeruginosa in complex with a synthetic thio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g3r
TitleLecA from Pseudomonas aeruginosa in complex with a synthetic thiogalactoside
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion / LecA / PA-IL / galactose-binding
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 1-thio-beta-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMelicher, F. / Faltinek, L. / Wimmerova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
CitationJournal: Chemistry / Year: 2025
Title: Bispecific Thio-Linked Disaccharides as Inhibitors of Pseudomonas Aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy.
Authors: Faltinek, L. / Melicher, F. / Kelemen, V. / Mezo, E. / Borbas, A. / Wimmerova, M.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
E: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
H: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,03027
Polymers102,1618
Non-polymers2,86919
Water6,359353
1
A: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
hetero molecules

D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50013
Polymers51,0814
Non-polymers1,4199
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
H: PA-I galactophilic lectin
hetero molecules

E: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,53014
Polymers51,0814
Non-polymers1,45010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)50.900, 99.823, 86.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
PA-I galactophilic lectin / PA-IL / Galactose-binding lectin


Mass: 12770.137 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097

-
Sugars , 2 types, 8 molecules

#2: Polysaccharide
1-thio-beta-D-galactopyranose-(1-1)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 342.362 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][a-L-Fucp]{[(1+S)][b-D-Galp1SH]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-YIO / 1-thio-beta-D-galactopyranose / (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL / 1-thio-beta-D-galactose / 1-thio-D-galactose / 1-thio-galactose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5S
IdentifierTypeProgram
b-D-Galp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 364 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, PEG 1000, magnesium chloride, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→49.91 Å / Num. obs: 93512 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 13554 / CC1/2: 0.834 / Rpim(I) all: 0.281 / Rrim(I) all: 0.751 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
SCALAdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.386 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.48 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 4735 5.065 %
Rwork0.196 88746 -
all0.198 --
obs-93481 98.177 %
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: 19.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.271 Å20 Å2-0.174 Å2
2--1.105 Å20 Å2
3----1.375 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 169 353 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166899
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.75710430
X-RAY DIFFRACTIONr_angle_other_deg0.5491.72515873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.526516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.176101030
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.49510320
X-RAY DIFFRACTIONr_chiral_restr0.0790.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021738
X-RAY DIFFRACTIONr_nbd_refined0.2010.21084
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25660
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23706
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.231
X-RAY DIFFRACTIONr_nbd_other0.280.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.214
X-RAY DIFFRACTIONr_mcbond_it1.6581.8963900
X-RAY DIFFRACTIONr_mcbond_other1.6581.8963900
X-RAY DIFFRACTIONr_mcangle_it2.4123.4094870
X-RAY DIFFRACTIONr_mcangle_other2.4123.414871
X-RAY DIFFRACTIONr_scbond_it2.172.1543702
X-RAY DIFFRACTIONr_scbond_other2.1692.1543703
X-RAY DIFFRACTIONr_scangle_it3.3423.8575542
X-RAY DIFFRACTIONr_scangle_other3.3413.8575543
X-RAY DIFFRACTIONr_lrange_it4.22620.127888
X-RAY DIFFRACTIONr_lrange_other4.22620.1217889
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
1.7-1.7440.3023710.24364830.24769870.9510.96598.09650.227
1.744-1.7920.2463230.22263640.22368030.960.9798.29490.204
1.792-1.8440.263100.21162720.21366760.9570.97398.5920.193
1.844-1.90.2733490.20259930.20664680.9530.97598.05190.187
1.9-1.9630.2582790.19259350.19562910.9590.97798.7760.177
1.963-2.0310.213160.19354790.19460250.9730.97796.18260.183
2.031-2.1080.2292740.19554210.19758570.9670.97797.23410.186
2.108-2.1940.2393030.19652710.19856340.9670.97798.9350.189
2.194-2.2910.2432320.19251320.19554190.9640.97898.98510.186
2.291-2.4030.2382590.18748740.1951750.9670.97999.18840.183
2.403-2.5320.2392100.18946350.19248940.9620.97898.99880.188
2.532-2.6850.2092430.18743500.18846510.9720.97898.7530.189
2.685-2.870.2532270.20240280.20443740.960.97497.27940.206
2.87-3.0990.2422390.21736860.21940690.9620.9796.4610.223
3.099-3.3930.2112020.21135550.21137770.9710.97499.47050.224
3.393-3.7910.2071550.231850.233750.9760.97898.9630.212
3.791-4.3720.1811480.16628440.16730230.980.98598.97450.189
4.372-5.3420.1871270.16523800.16625590.9870.98797.9680.19
5.342-7.5030.2341040.19917970.20120040.9790.98494.86030.228
7.503-45.3860.244640.21310620.21511520.9710.97497.74310.239

+
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