[English] 日本語
Yorodumi
- PDB-8qww: Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qww
TitleStructure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol without TFA
ComponentsPeptide LYIQWL from Tc5b
KeywordsPROTEIN FIBRIL / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDurvanger, Z.
Funding support Hungary, European Union, 3items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ Hungary
CitationJournal: Commun Biol / Year: 2024
Title: Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology.
Authors: Durvanger, Z. / Bencs, F. / Menyhard, D.K. / Horvath, D. / Perczel, A.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b


Theoretical massNumber of molelcules
Total (without water)1,6702
Polymers1,6702
Non-polymers00
Water181
1
A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b

A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b

A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b

A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b

A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b


Theoretical massNumber of molelcules
Total (without water)8,35010
Polymers8,35010
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
Unit cell
Length a, b, c (Å)4.874, 42.270, 21.442
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein/peptide Peptide LYIQWL from Tc5b


Mass: 835.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 310 K / Method: evaporation, recrystallization
Details: The peptide was dissolved in 10 v/v% ethanol at 0.5 mg/ml concentration and incubated at 310K.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→19.05 Å / Num. obs: 1372 / % possible obs: 97.93 % / Redundancy: 3.28 % / Biso Wilson estimate: 6.35 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.101 / Net I/σ(I): 7.5
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 132 / CC1/2: 0.727 / Rrim(I) all: 0.567 / % possible all: 88

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.05 Å / SU ML: 0.0897 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.7021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1737 144 10.57 %
Rwork0.1357 1218 -
obs0.1396 1362 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms120 0 0 1 121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061142
X-RAY DIFFRACTIONf_angle_d1.158196
X-RAY DIFFRACTIONf_chiral_restr0.059922
X-RAY DIFFRACTIONf_plane_restr0.004622
X-RAY DIFFRACTIONf_dihedral_angle_d22.707418
LS refinement shellResolution: 1.5→19.05 Å
RfactorNum. reflection% reflection
Rfree0.1737 144 -
Rwork0.1357 1218 -
obs--97.22 %
Refinement TLS params.Method: refined / Origin x: 1.95823275698 Å / Origin y: 4.03530295693 Å / Origin z: 5.48028424488 Å
111213212223313233
T0.0210081661851 Å20.00119098604604 Å20.000581513896195 Å2-0.0359464454954 Å20.00377339022949 Å2--0.0294076084929 Å2
L0.826088444931 °20.0830696652301 °2-0.0224214660718 °2-0.666668015909 °20.00507312991613 °2--1.07119377632 °2
S0.00848117255155 Å °0.0808012469916 Å °-0.00927489635971 Å °-0.0431071292577 Å °0.0427622927918 Å °0.00109494805781 Å °0.0191558702217 Å °-0.0308783343564 Å °2.47552853789 Å °
Refinement TLS groupSelection details: all

+
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