[English] 日本語
Yorodumi
- PDB-6yo3: LecA from Pseudomonas aeruginosa in complex with a catechol CAS n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yo3
TitleLecA from Pseudomonas aeruginosa in complex with a catechol CAS no. 67984-81-0
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Non-carbohydrate glycomimetics / PAINS / lectin / catechols
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
2,3-bis(oxidanyl)benzenecarbonitrile / TRIETHYLENE GLYCOL / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKuhaudomlarp, S. / Imberty, A. / Titz, A.
Funding support France, Germany, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-AAPG-2017 France
French National Research AgencyANR-17-CE11-0048 France
German Research Foundation (DFG)Ti756/5-1 Germany
German Research Foundation (DFG)RA1944/7-1 Germany
French National Research AgencyANR-17-EURE-0003 France
French National Research AgencyANR-15-IDEX02 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Non-Carbohydrate Glycomimetics as Inhibitors of Calcium(II)-Binding Lectins.
Authors: Kuhaudomlarp, S. / Siebs, E. / Shanina, E. / Topin, J. / Joachim, I. / da Silva Figueiredo Celestino Gomes, P. / Varrot, A. / Rognan, D. / Rademacher, C. / Imberty, A. / Titz, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26215
Polymers51,0814
Non-polymers1,18111
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-17 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.943, 48.630, 128.632
Angle α, β, γ (deg.)90.000, 95.590, 90.000
Int Tables number5
Space group name H-MI121

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LecA from Pseudomonas aeruginosa was produced as a recombinant protein in E. coli
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097

-
Non-polymers , 7 types, 364 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P3K / 2,3-bis(oxidanyl)benzenecarbonitrile


Mass: 135.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound ...Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound for co-crystallisation

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.84→45.5 Å / Num. obs: 47830 / % possible obs: 99.6 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.041 / Rrim(I) all: 0.099 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.880.521583529070.9190.240.5752.797.2
9-45.460.04823744400.9980.0220.05325.397.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.84→45.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.711 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2432 5.1 %RANDOM
Rwork0.1723 ---
obs0.1741 45394 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.6 Å2 / Biso mean: 21.456 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å21.52 Å2
2--0.77 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 1.84→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 74 363 4034
Biso mean--32.2 29.82 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173313
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6365186
X-RAY DIFFRACTIONr_angle_other_deg1.431.5827726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51725.088171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.296158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
LS refinement shellResolution: 1.84→1.885 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.276 163 -
Rwork0.246 3307 -
obs--97.66 %

+
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://pdbjlvh1.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