[English] 日本語
Yorodumi
- PDB-4yw6: Structural Insight into Divalent Galactoside Binding to Pseudomon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yw6
TitleStructural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Galactosides / lectins
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 lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-G0P / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVisini, R. / Jin, X. / Michaud, G. / Bergmann, M. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R. / Reymond, J.-L.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structural Insight into Multivalent Galactoside Binding to Pseudomonas aeruginosa Lectin LecA.
Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. ...Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R.J. / Reymond, J.L.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
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)53,16712
Polymers51,0814
Non-polymers2,0868
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-3 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.870, 72.980, 79.020
Angle α, β, γ (deg.)117.520, 104.990, 90.000
Int Tables number1
Space group name H-MP1

-
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
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-G0P / N-[(2S)-6-amino-1-oxo-1-(pyrrolidin-1-yl)hexan-2-yl]-4-(beta-D-galactopyranosyloxy)benzamide


Mass: 481.539 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H35N3O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.5M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.4→67.032 Å / Num. all: 129508 / Num. obs: 129508 / % possible obs: 84.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.45 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Rsym value: 0.058 / Net I/av σ(I): 4.983 / Net I/σ(I): 7.7 / Num. measured all: 380562
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.482.90.2671.153158180560.1940.2673.581.1
1.48-1.572.80.221.143973156370.1680.22474.1
1.57-1.672.90.0877.153820188220.0610.0875.694.9
1.67-1.813.20.0825.156121176140.0540.0827.295.5
1.81-1.9830.1092.535286117220.0760.1098.268.9
1.98-2.212.60.0752.932745128160.060.0759.383.8
2.21-2.562.90.0634.333615117820.0450.06310.786.7
2.56-3.133.20.0510.233324105670.0330.0512.292.7
3.13-4.433.10.0413.22427977340.0260.0413.487.5
4.43-23.93430.03413.51424147580.0240.0341398.6

-
Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1oko

1oko


Resolution: 1.4→23.934 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 1961 1.54 %
Rwork0.1861 125153 -
obs0.1864 127114 83.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.37 Å2 / Biso mean: 18.9842 Å2 / Biso min: 4.8 Å2
Refinement stepCycle: final / Resolution: 1.4→23.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 280 898 4782
Biso mean--41.5 30.73 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093847
X-RAY DIFFRACTIONf_angle_d1.3795263
X-RAY DIFFRACTIONf_chiral_restr0.082569
X-RAY DIFFRACTIONf_plane_restr0.007690
X-RAY DIFFRACTIONf_dihedral_angle_d13.4621311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4350.2771510.21349774992591
1.435-1.47380.41511200.4117099721967
1.4738-1.51720.31381070.2837286739367
1.5172-1.56610.24251290.27917558768771
1.5661-1.62210.2141590.1623101091026895
1.6221-1.6870.17311530.1446103091046295
1.687-1.76380.19641610.1649101071026895
1.7638-1.85670.15831530.1542102651041896
1.8567-1.9730.2035920.22525551564352
1.973-2.12530.23421240.20378422854678
2.1253-2.3390.22411360.18648678881481
2.339-2.6770.19331490.1768101691031897
2.677-3.37130.20061620.1726101991036198
3.3713-23.93790.17431650.16149627979290

+
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