[English] 日本語
Yorodumi
- PDB-7z63: Structure of the LecA lectin from Pseudomonas aeruginosa in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z63
TitleStructure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / lectin / antiadhesive / thiogalactoside / RNA BINDING PROTEIN
Function / homology
Function and homology information


heterophilic cell-cell adhesion / 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
Chem-IE3 / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVarrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Discovery of potent 1,1-diarylthiogalactoside glycomimetic inhibitors of Pseudomonas aeruginosa LecA with antibiofilm properties.
Authors: Bruneau, A. / Gillon, E. / Furiga, A. / Brachet, E. / Alami, M. / Roques, C. / Varrot, A. / Imberty, A. / Messaoudi, S.
History
DepositionMar 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: PA-I galactophilic lectin
BBB: PA-I galactophilic lectin
CCC: PA-I galactophilic lectin
DDD: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,28913
Polymers51,0814
Non-polymers2,2089
Water15,006833
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint1 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 61.932, 180.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#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: N terminal methionine cleaved / Source: (gene. exp.) Pseudomonas aeruginosa 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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IE3 / [3-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-4-methoxy-phenyl]-(3,4,5-trimethoxyphenyl)methanone


Mass: 496.527 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H28O10S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.87 % / Description: rod
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the ...Details: LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the supernatant after centrifugation at 20000 g for 5 minutes since precipitation was observed and a crystallization solution containing 18% PEG3350, 150 mM potassium thiocyanate (KSCN) and 100 mM Tris HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→45 Å / Num. obs: 48775 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2627 / CC1/2: 0.976 / Rpim(I) all: 0.186 / Rrim(I) all: 0.347 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.75→43.131 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.267 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2074 2506 5.146 %
Rwork0.1613 46191 -
all0.164 --
obs-48697 99.938 %
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: 13.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.167 Å2-0 Å2-0 Å2
2--0.827 Å2-0 Å2
3----1.995 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 133 833 4568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133889
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163491
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.6795333
X-RAY DIFFRACTIONr_angle_other_deg1.571.6158027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99625.172174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.676158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined0.1990.2671
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23232
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21933
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2524
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.210
X-RAY DIFFRACTIONr_nbd_other0.1880.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.256
X-RAY DIFFRACTIONr_mcbond_it1.5091.1431967
X-RAY DIFFRACTIONr_mcbond_other1.5051.1421966
X-RAY DIFFRACTIONr_mcangle_it2.1171.7092464
X-RAY DIFFRACTIONr_mcangle_other2.1181.7092465
X-RAY DIFFRACTIONr_scbond_it2.1571.3731922
X-RAY DIFFRACTIONr_scbond_other2.1581.3731923
X-RAY DIFFRACTIONr_scangle_it3.1661.9872869
X-RAY DIFFRACTIONr_scangle_other3.1651.9872870
X-RAY DIFFRACTIONr_lrange_it4.88923.69717443
X-RAY DIFFRACTIONr_lrange_other4.30622.27216262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2422070.2053311X-RAY DIFFRACTION99.9432
1.795-1.8450.2241880.1763281X-RAY DIFFRACTION99.9712
1.845-1.8980.2411700.1743177X-RAY DIFFRACTION100
1.898-1.9560.251770.1733080X-RAY DIFFRACTION99.9386
1.956-2.020.2181660.1583046X-RAY DIFFRACTION100
2.02-2.0910.2221520.1622887X-RAY DIFFRACTION99.9671
2.091-2.170.211620.1572803X-RAY DIFFRACTION100
2.17-2.2580.2121580.1592695X-RAY DIFFRACTION100
2.258-2.3580.211200.1552657X-RAY DIFFRACTION99.964
2.358-2.4730.1921390.1482514X-RAY DIFFRACTION100
2.473-2.6060.2151340.1592357X-RAY DIFFRACTION100
2.606-2.7640.2181150.1532267X-RAY DIFFRACTION100
2.764-2.9540.21160.1592117X-RAY DIFFRACTION99.9105
2.954-3.1890.191900.1562023X-RAY DIFFRACTION100
3.189-3.4920.218870.1511864X-RAY DIFFRACTION100
3.492-3.9010.184850.1681694X-RAY DIFFRACTION100
3.901-4.4990.176760.1481482X-RAY DIFFRACTION100
4.499-5.4970.16680.1481295X-RAY DIFFRACTION99.7074
5.497-7.7160.191590.1781025X-RAY DIFFRACTION99.724

+
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