[English] 日本語
Yorodumi
- PDB-6s5s: Cfucosylated second generation peptide dendrimer SBD8 bound to Fu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5s
TitleCfucosylated second generation peptide dendrimer SBD8 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.43 Angstrom resolution
Components
  • Fucose-binding lectin
  • SBD8 chain B
  • SBD8 chain C
  • SBD8 chain D
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated / Dendrimer / Second Generation
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMINO GROUP / Chem-ZDC / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.433 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Helv.Chim.Acta / Year: 2019
Title: X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB
Authors: Baeriswyl, S. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / refine / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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: Fucose-binding lectin
B: SBD8 chain B
C: SBD8 chain C
D: SBD8 chain D
E: SBD8 chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4099
Polymers14,1075
Non-polymers3024
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-25 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.297, 106.297, 57.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-533-

HOH

31A-546-

HOH

-
Components

-
Protein/peptide , 3 types, 4 molecules BCED

#2: Protein/peptide SBD8 chain B


Mass: 806.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain B / Source: (synth.) unidentified (others)
#3: Protein/peptide SBD8 chain C


Mass: 357.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain C / Source: (synth.) unidentified (others)
#4: Protein/peptide SBD8 chain D


Mass: 719.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain D / Source: (synth.) unidentified (others)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fucose binding lectin LecB (PA-IIL) from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#7: Sugar ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 3 types, 162 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 3.0 M Sodium chloride

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.433→48.517 Å / Num. obs: 66042 / % possible obs: 99.5 % / Redundancy: 17.1 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 14.8
Reflection shellResolution: 1.433→1.44 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 10408 / CC1/2: 0.247 / Rrim(I) all: 0.207 / % possible all: 99.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.94 Å48.52 Å
Translation4.94 Å48.52 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.433→48.517 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.1785 3292 4.99 %
Rwork0.1628 --
obs0.1636 66035 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.33 Å2 / Biso mean: 20.9158 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 1.433→48.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 5 159 1141
Biso mean--19.98 31.47 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017994
X-RAY DIFFRACTIONf_angle_d1.5641349
X-RAY DIFFRACTIONf_chiral_restr0.162170
X-RAY DIFFRACTIONf_plane_restr0.012178
X-RAY DIFFRACTIONf_dihedral_angle_d17.03333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4329-1.45340.43851300.37292411254192
1.4534-1.47510.34561310.3472512264397
1.4751-1.49810.30081420.301426462788100
1.4981-1.52270.26631370.273725942731100
1.5227-1.54890.27191390.244826702809100
1.5489-1.57710.26051380.237326202758100
1.5771-1.60740.24061360.226426062742100
1.6074-1.64020.23221390.216926362775100
1.6402-1.67590.2271350.192826512786100
1.6759-1.71490.19471390.180526092748100
1.7149-1.75780.1761390.173525862725100
1.7578-1.80530.1831380.155826552793100
1.8053-1.85840.16171410.145926252766100
1.8584-1.91840.13951340.142226252759100
1.9184-1.9870.16541360.138426262762100
1.987-2.06650.18791350.130226272762100
2.0665-2.16060.15141390.126626302769100
2.1606-2.27450.16111350.129726312766100
2.2745-2.4170.12091420.128926232765100
2.417-2.60360.15631390.140326342773100
2.6036-2.86560.16081360.144726242760100
2.8656-3.28020.15011400.146626132753100
3.2802-4.13240.15371370.134226462783100
4.1324-48.54510.18221350.180426432778100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.263-0.2876-0.86750.4837-0.11541.4446-0.00050.01030.0504-0.00870.0026-0.079-0.00030.0077-0.00070.1184-0.0098-0.02290.0806-0.02020.0997-46.547212.12366.9707
27.3825-0.6153-0.46350.14550.4011.0858-0.0683-0.1355-0.00660.030.0937-0.0313-0.0320.0174-0.03230.1487-0.0013-0.00990.0709-0.00310.1265-47.703819.1619.5727
36.0665-2.3183-5.27311.7891.78454.6748-0.2803-0.3602-0.370.16530.1305-0.02240.18610.25590.06880.1450.0129-0.02160.17780.00240.1395-41.745911.560611.8519
46.35962.43331.45971.97641.05350.5722-0.3547-1.15770.69871.4075-0.04990.331-0.6297-0.66410.28040.4180.0879-0.03370.268-0.05840.1623-53.8815.450123.2521
50.8943-0.8096-0.54731.63051.37461.4837-0.0611-0.0419-0.00720.09050.06730.00390.0756-0.00310.00330.13190.0032-0.00420.08930.01090.0927-53.60916.88836.8228
62.463-0.0133-1.85080.790.24281.9639-0.07590.1220.0196-0.01780.0767-0.02250.0323-0.05250.00060.1464-0.0033-0.00240.1222-0.00220.1155-46.41812.2790.3297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 56 )A26 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 69 )A57 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )A70 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 104 )A75 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 114 )A105 - 114

+
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