[English] 日本語
Yorodumi
- PDB-6c4o: AMYLOID FORMING PEPTIDE TIAALLS FROM TRANSTHYRETIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c4o
TitleAMYLOID FORMING PEPTIDE TIAALLS FROM TRANSTHYRETIN
ComponentsTHR-ILE-ALA-ALA-LEU-LEU-SER
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSievers, S.A. / Sawaya, M.R. / Saelices, L. / Eisenberg, D.S.
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structures of amyloidogenic segments of human transthyretin.
Authors: Saelices, L. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D.S.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THR-ILE-ALA-ALA-LEU-LEU-SER
B: THR-ILE-ALA-ALA-LEU-LEU-SER


Theoretical massNumber of molelcules
Total (without water)1,3762
Polymers1,3762
Non-polymers00
Water905
1
A: THR-ILE-ALA-ALA-LEU-LEU-SER
B: THR-ILE-ALA-ALA-LEU-LEU-SER
x 10


Theoretical massNumber of molelcules
Total (without water)13,75720
Polymers13,75720
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_355-x-2,y+1/2,-z1
crystal symmetry operation2_255-x-3,y+1/2,-z1
Unit cell
Length a, b, c (Å)9.597, 17.306, 24.998
Angle α, β, γ (deg.)90.000, 95.760, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide THR-ILE-ALA-ALA-LEU-LEU-SER


Mass: 687.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.5 Å3/Da / Density % sol: 18.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: TIAALLS crystals were grown from 5mg/mL peptide and 10% acetonitrile. The reservoir contained 100mM Tris pH 8.5 and 0.3 M magnesium formate dihydrate. Crystals were soaked on 25% Glycerol prior to diffraction

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→90 Å / Num. obs: 784 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.217 / Χ2: 1.079 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.942.80.5561551.002193.4
1.94-2.133.50.4291451.124199.3
2.13-2.443.70.3251591.019198.1
2.44-3.083.90.2121591.159197.5
3.08-903.70.1371661.065199.4

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.4.0061refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→14.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.189 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 85 10.9 %RANDOM
Rwork0.1821 ---
obs0.1869 692 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 35.06 Å2 / Biso mean: 6.636 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.2 Å2
2--0.85 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.79→14.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms96 0 0 5 101
Biso mean---27.11 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0250
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.108128
X-RAY DIFFRACTIONr_angle_other_deg0.8583130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.111512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2641516
X-RAY DIFFRACTIONr_chiral_restr0.0860.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0292
X-RAY DIFFRACTIONr_gen_planes_other00.0212
LS refinement shellResolution: 1.794→1.839 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.76 5 -
Rwork0.187 43 -
all-48 -
obs--72.73 %

+
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