[English] 日本語
Yorodumi
- PDB-5nf0: Discovery, crystal structures and atomic force microscopy study o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nf0
TitleDiscovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa
Components
  • CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
  • Fragment of ligand
  • Fucose-binding lectin II (PA-IIL)
KeywordsANTIMICROBIAL PROTEIN / Cyclic peptides / Antimicrobials / Pseudomonas aeruginosa
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ORTHO-XYLENE / Chem-ZDC / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.271 Å
AuthorsReymond, J.-L. / Darbre, T. / Stocker, A. / Hong, W. / van Delden, C. / Koehler, T. / Luscher, A. / Visini, R. / Fu, Y. / Di Bonaventura, I. / He, R.
CitationJournal: Chem Sci / Year: 2017
Title: Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.
Authors: He, R. / Di Bonaventura, I. / Visini, R. / Gan, B.H. / Fu, Y. / Probst, D. / Luscher, A. / Kohler, T. / van Delden, C. / Stocker, A. / Hong, W. / Darbre, T. / Reymond, J.L.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / refine_hist / 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_hist.d_res_low / _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 1.3Jan 17, 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 II (PA-IIL)
B: Fucose-binding lectin II (PA-IIL)
C: Fucose-binding lectin II (PA-IIL)
D: Fucose-binding lectin II (PA-IIL)
E: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
F: Fragment of ligand
G: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
H: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53923
Polymers52,0758
Non-polymers1,46415
Water10,647591
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: already known by first crystallization. Well known protein in literature
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-82 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.278, 99.966, 106.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein/peptide , 2 types, 4 molecules EGHF

#2: Protein/peptide CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY


Mass: 1611.033 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Fragment of ligand


Mass: 303.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
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
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713
Production host: Escherichia coli (E. coli) / 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, 602 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.005 M Cadmium chloride hydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.27→47.03 Å / Num. obs: 120367 / % possible obs: 94.1 % / Redundancy: 3.31 % / Rrim(I) all: 0.058 / Net I/σ(I): 13.95
Reflection shellResolution: 1.27→1.35 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 18173 / Num. unique obs: 58803 / CC1/2: 0.851 / Rrim(I) all: 0.615 / % possible all: 88.8

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.271→47.03 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 11349 5.01 %
Rwork0.1628 --
obs0.1639 226635 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.271→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 84 591 4303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113774
X-RAY DIFFRACTIONf_angle_d1.265150
X-RAY DIFFRACTIONf_dihedral_angle_d14.3231210
X-RAY DIFFRACTIONf_chiral_restr0.126625
X-RAY DIFFRACTIONf_plane_restr0.008662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.271-1.28550.30913390.28296373X-RAY DIFFRACTION81
1.2855-1.30060.25183550.27626665X-RAY DIFFRACTION86
1.3006-1.31640.29343640.26526801X-RAY DIFFRACTION88
1.3164-1.33310.29723680.25776923X-RAY DIFFRACTION88
1.3331-1.35070.29693510.26046775X-RAY DIFFRACTION88
1.3507-1.36920.28653490.25436655X-RAY DIFFRACTION85
1.3692-1.38870.24833600.23756800X-RAY DIFFRACTION88
1.3887-1.40940.24883620.22556865X-RAY DIFFRACTION87
1.4094-1.43150.23863650.21896962X-RAY DIFFRACTION90
1.4315-1.45490.26343730.21977074X-RAY DIFFRACTION90
1.4549-1.480.20813730.20597163X-RAY DIFFRACTION92
1.48-1.50690.20563790.20297156X-RAY DIFFRACTION92
1.5069-1.53590.20883790.18357254X-RAY DIFFRACTION93
1.5359-1.56730.20573880.17457313X-RAY DIFFRACTION93
1.5673-1.60140.19883790.1657237X-RAY DIFFRACTION94
1.6014-1.63860.16663900.16337436X-RAY DIFFRACTION94
1.6386-1.67960.1853880.15857358X-RAY DIFFRACTION94
1.6796-1.7250.19223900.16127408X-RAY DIFFRACTION95
1.725-1.77580.20363910.1557319X-RAY DIFFRACTION94
1.7758-1.83310.17183730.1517026X-RAY DIFFRACTION90
1.8331-1.89860.17953890.1477319X-RAY DIFFRACTION94
1.8986-1.97460.15923910.13357403X-RAY DIFFRACTION95
1.9746-2.06450.14553920.13167546X-RAY DIFFRACTION97
2.0645-2.17330.15234000.13377536X-RAY DIFFRACTION97
2.1733-2.30950.17073940.14527494X-RAY DIFFRACTION96
2.3095-2.48780.19714030.15067536X-RAY DIFFRACTION97
2.4878-2.73820.1533930.1547552X-RAY DIFFRACTION97
2.7382-3.13430.17463860.15467293X-RAY DIFFRACTION93
3.1343-3.94860.1713780.14277374X-RAY DIFFRACTION95
3.9486-47.06840.16014070.15267670X-RAY DIFFRACTION98

+
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