[English] 日本語
Yorodumi
- PDB-6cg3: Macrocyclic peptide derived from Abeta(17-36) - (ORN)LV(PHI)FAED(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cg3
TitleMacrocyclic peptide derived from Abeta(17-36) - (ORN)LV(PHI)FAED(ORN)AII(2-nitrobenzylglycine)L(ORN)V
ComponentsORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
KeywordsNEUROPEPTIDE / Amyloid / oligomer / Alzheimer's Disease / Abeta
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.03 Å
AuthorsSalveson, P.J. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Controlling the Oligomerization State of A beta-Derived Peptides with Light.
Authors: Salveson, P.J. / Haerianardakani, S. / Thuy-Boun, A. / Kreutzer, A.G. / Nowick, J.S.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL


Theoretical massNumber of molelcules
Total (without water)2,0101
Polymers2,0101
Non-polymers00
Water19811
1
A: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
x 12


Theoretical massNumber of molelcules
Total (without water)24,12112
Polymers24,12112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area9530 Å2
ΔGint-79 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.504, 47.504, 47.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

-
Components

#1: Protein/peptide ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL


Mass: 2010.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 8.75 18% Jeffamine M-600

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.03→19.4 Å / Num. obs: 2241 / % possible obs: 99.5 % / Redundancy: 28.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Net I/σ(I): 18.4
Reflection shellResolution: 2.08→2.13 Å / Rmerge(I) obs: 0.654 / Num. unique obs: 312 / CC1/2: 0.954 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→19.393 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.2547 232 10.35 %
Rwork0.2113 --
obs0.2159 2241 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→19.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 0 0 11 145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004137
X-RAY DIFFRACTIONf_angle_d1.164183
X-RAY DIFFRACTIONf_dihedral_angle_d27.47189
X-RAY DIFFRACTIONf_chiral_restr0.12421
X-RAY DIFFRACTIONf_plane_restr0.00322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0293-2.55570.28321140.243990X-RAY DIFFRACTION98
2.5557-19.39430.24311180.19791019X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.592 Å / Origin y: 21.6263 Å / Origin z: 13.5085 Å
111213212223313233
T0.1603 Å2-0.0241 Å2-0.01 Å2-0.2325 Å2-0.0505 Å2--0.2055 Å2
L1.3393 °20.5108 °2-0.6032 °2-2.8083 °2-0.1937 °2--2.3496 °2
S0.1743 Å °-0.2979 Å °0.2919 Å °0.0122 Å °-0.0535 Å °-0.3814 Å °-0.5291 Å °0.3168 Å °-0.0206 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 16 )

+
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