[English] 日本語
Yorodumi
- PDB-6q79: Structure of Fucosylated D-antimicrobial peptide SB4 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q79
TitleStructure of Fucosylated D-antimicrobial peptide SB4 in complex with the Fucose-binding lectin PA-IIL at 2.009 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB4
  • SB4 incomplete
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
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 / polypeptide(D) / polypeptide(D) (> 10) / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.009 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionDec 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / 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 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
E: SB4
B: Fucose-binding lectin
F: SB4 incomplete
C: Fucose-binding lectin
G: SB4 incomplete
D: Fucose-binding lectin
H: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,70622
Polymers51,5298
Non-polymers1,17714
Water6,017334
1
A: Fucose-binding lectin
E: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6227
Polymers13,2802
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin
F: SB4 incomplete
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8116
Polymers12,4852
Non-polymers3264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin
G: SB4 incomplete
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7314
Polymers12,4852
Non-polymers2462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fucose-binding lectin
H: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5425
Polymers13,2802
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.422, 64.124, 68.960
Angle α, β, γ (deg.)90.000, 104.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Polypeptide(D) , 2 types, 4 molecules EHFG

#2: Polypeptide(D) SB4


Mass: 1545.013 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Fucosylated D-antimicrobial peptide SB4, complete alpha helical sequence
Source: (synth.) synthetic construct (others)
#3: Polypeptide(D) SB4 incomplete


Mass: 749.943 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Fucosylated D-antimicrobial peptide SB4, incompletely resolved structure. Full sequence: (DLY)(DTY)(DLY)(DLY)(DAL)(DLE)(DLY)(DLY)(DLE)(DAL)(DLY)(DLE)(DLE)
Source: (synth.) synthetic construct (others)

-
Protein / Sugars , 2 types, 8 molecules ABCD

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


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin PA-IIL Lectin B from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, 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
#5: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6

-
Non-polymers , 3 types, 344 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.009→41.629 Å / Num. all: 31842 / Num. obs: 31842 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Rsym value: 0.066 / Net I/av σ(I): 9.5 / Net I/σ(I): 12.4 / Num. measured all: 107976
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.01-2.123.30.4631.71495345580.3010.5540.4632.898.2
2.12-2.253.50.3422.31557944090.2130.4030.3423.899.7
2.25-2.43.50.243.31429540900.150.2830.245.299.8
2.4-2.593.40.1684.71327838700.1070.1990.1686.999.8
2.59-2.843.20.17.71115835270.0670.1210.19.999.8
2.84-3.183.40.06511.61088532260.0410.0770.06515100
3.18-3.673.50.04315.7999328250.0270.050.04323.899.6
3.67-4.493.40.03518823824050.0220.0420.03529.299.4
4.49-6.353.10.0318.1581018790.020.0370.0331.199.8
6.35-41.6293.60.02718.4378710530.0160.0310.02736.199.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å41.63 Å
Translation2.96 Å41.63 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.009→41.629 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 3012 4.98 %
Rwork0.1543 57461 -
obs0.1582 31819 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.16 Å2 / Biso mean: 38.007 Å2 / Biso min: 17.18 Å2
Refinement stepCycle: final / Resolution: 2.009→41.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 62 334 3985
Biso mean--38.38 41.71 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063687
X-RAY DIFFRACTIONf_angle_d0.8255044
X-RAY DIFFRACTIONf_chiral_restr0.059637
X-RAY DIFFRACTIONf_plane_restr0.003660
X-RAY DIFFRACTIONf_dihedral_angle_d6.4342057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0092-2.04060.34771260.25062452257890
2.0406-2.0740.35181340.24612589272396
2.074-2.10980.33631380.23072614275297
2.1098-2.14810.3121360.21472688282497
2.1481-2.18950.28771410.20012639278097
2.1895-2.23410.26241310.1982604273597
2.2341-2.28270.31291380.18582615275397
2.2827-2.33580.29231390.1812615275497
2.3358-2.39420.27221390.16842607274698
2.3942-2.45890.28431410.17012681282297
2.4589-2.53130.27371300.17292572270297
2.5313-2.6130.22031390.14922610274997
2.613-2.70640.28491360.15622616275295
2.7064-2.81470.24811290.14882508263794
2.8147-2.94280.22091380.14682657279597
2.9428-3.09790.24921390.13952635277498
3.0979-3.29190.25241400.15022629276998
3.2919-3.54590.21341410.13472631277298
3.5459-3.90250.22671360.12652601273797
3.9025-4.46670.19271440.12462628277298
4.4667-5.62530.13291380.12922603274196
5.6253-41.63840.2151390.1562667280699

+
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