[English] 日本語
Yorodumi
- PDB-2ona: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ona
TitleMVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
ComponentsMVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
KeywordsPROTEIN FIBRIL / steric zipper / beta sheet
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSambashivan, S. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
B: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
C: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
D: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40


Theoretical massNumber of molelcules
Total (without water)2,2434
Polymers2,2434
Non-polymers00
Water1086
1
A: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
B: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
C: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
D: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40

A: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
B: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
C: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
D: MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40


Theoretical massNumber of molelcules
Total (without water)4,4868
Polymers4,4868
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)25.862, 9.699, 15.851
Angle α, β, γ (deg.)77.180, 74.690, 86.930
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis.

-
Components

#1: Protein/peptide
MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40


Mass: 560.707 Da / Num. of mol.: 4 / Fragment: residues 35-40 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30 mg/mL peptide in water mixed 1:1 with reservoir containing 0.02 M CaCl2, 30% MPD, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 2→90 Å / Num. obs: 409 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 1.6 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.16 / Χ2: 1.068 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.15 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.222 / Num. unique all: 163 / Χ2: 1.124 / % possible all: 94.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine idealized beta strand

Resolution: 2.03→24.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.305 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 44 10.8 %RANDOM
Rwork0.202 ---
obs0.211 409 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.28 Å20.26 Å2
2--0.1 Å2-0.07 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.03→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms152 0 0 6 158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0280
X-RAY DIFFRACTIONr_angle_refined_deg1.2542.057196
X-RAY DIFFRACTIONr_angle_other_deg0.6693204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.56520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4571524
X-RAY DIFFRACTIONr_chiral_restr0.0840.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0220
X-RAY DIFFRACTIONr_nbd_refined0.1590.219
X-RAY DIFFRACTIONr_nbd_other0.180.262
X-RAY DIFFRACTIONr_nbtor_refined0.140.266
X-RAY DIFFRACTIONr_nbtor_other0.0850.299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.22
X-RAY DIFFRACTIONr_mcbond_it1.7322137
X-RAY DIFFRACTIONr_mcbond_other0.456252
X-RAY DIFFRACTIONr_mcangle_it1.8213176
X-RAY DIFFRACTIONr_scbond_it2.08237
X-RAY DIFFRACTIONr_scangle_it2.628320
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A33MEDIUM POSITIONAL0.490.5
2B33MEDIUM POSITIONAL0.550.5
3C33MEDIUM POSITIONAL0.140.5
4D33MEDIUM POSITIONAL0.170.5
1A25LOOSE POSITIONAL0.85
2B25LOOSE POSITIONAL1.035
3C25LOOSE POSITIONAL0.65
4D25LOOSE POSITIONAL0.55
1A33MEDIUM THERMAL0.462
2B33MEDIUM THERMAL0.492
3C33MEDIUM THERMAL0.542
4D33MEDIUM THERMAL0.692
1A25LOOSE THERMAL1.5710
2B25LOOSE THERMAL1.4110
3C25LOOSE THERMAL1.0310
4D25LOOSE THERMAL2.0910
LS refinement shellResolution: 2.03→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 1 -
Rwork0.208 24 -
obs-25 37.31 %

+
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