[English] 日本語
Yorodumi
- PDB-5e61: Structure of amyloid-forming peptide FGAILSS (residues 23-29) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5.0E+61
TitleStructure of amyloid-forming peptide FGAILSS (residues 23-29) from islet amyloid polypeptide
ComponentsFGAILSS (residues 23-29) from islet amyloid polypeptide
Keywordsde novo protein / membrane protein / amyloid-like protofibril / Protein Fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSoriaga, A.B. / Eisenberg, D.
CitationJournal: J.Phys.Chem.B / Year: 2016
Title: Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.
Authors: Soriaga, A.B. / Sangwan, S. / Macdonald, R. / Sawaya, M.R. / Eisenberg, D.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_ref_seq
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FGAILSS (residues 23-29) from islet amyloid polypeptide
B: FGAILSS (residues 23-29) from islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)1,3882
Polymers1,3882
Non-polymers00
Water00
1
A: FGAILSS (residues 23-29) from islet amyloid polypeptide
x 5
B: FGAILSS (residues 23-29) from islet amyloid polypeptide
x 6


Theoretical massNumber of molelcules
Total (without water)7,63211
Polymers7,63211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_545x,y-1,z2
crystal symmetry operation1_565x,y+1,z2
crystal symmetry operation1_655x+1,y,z2
crystal symmetry operation1_645x+1,y-1,z2
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)8.770, 9.500, 24.740
Angle α, β, γ (deg.)88.22, 80.00, 70.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide FGAILSS (residues 23-29) from islet amyloid polypeptide


Mass: 693.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.38 Å3/Da / Density % sol: 10.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6.4mg/ml in 20mM Lithium hydroxide and mixed with 0.1M HEPES pH 6.5 and 0.5M Sodium Formate

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→4.38 Å / Num. obs: 647 / % possible obs: 93.36 % / Redundancy: 5.217 % / Rmerge(I) obs: 0.241 / Net I/σ(I): 4.29
Reflection shellResolution: 1.79→1.96 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.4 / % possible all: 72.3

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→4.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.8 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 65 10 %RANDOM
Rwork0.16661 ---
obs0.17221 582 93.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.39 Å20.41 Å2
2---0.6 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.79→4.38 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 0 0 98
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0297
X-RAY DIFFRACTIONr_angle_refined_deg22.022130
X-RAY DIFFRACTIONr_angle_other_deg0.7643221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.168512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.404202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4851514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4871.95854
X-RAY DIFFRACTIONr_mcbond_other3.8971.84753
X-RAY DIFFRACTIONr_mcangle_it8.2682.75664
X-RAY DIFFRACTIONr_mcangle_other8.4452.83165
X-RAY DIFFRACTIONr_scbond_it4.9112.67844
X-RAY DIFFRACTIONr_scbond_other4.3052.57943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0833.81866
X-RAY DIFFRACTIONr_long_range_B_refined11.717.89491
X-RAY DIFFRACTIONr_long_range_B_other11.97718.33992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.788→1.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 2 -
Rwork0.331 22 -
obs--52.17 %

+
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://pdbjlvh1.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