[English] 日本語
Yorodumi
- PDB-6dr5: X-ray crystallographic structure of a covalent trimer derived fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dr5
TitleX-ray crystallographic structure of a covalent trimer derived from A-beta 17_36 containing the I31Chg point mutation
ComponentsORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
KeywordsDE NOVO PROTEIN / Amyloid / Alzheimers Disease / Abeta / oligomer
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.079 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)097562 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from A beta.
Authors: Salveson, P.J. / Haerianardakani, S. / Thuy-Boun, A. / Yoo, S. / Kreutzer, A.G. / Demeler, B. / Nowick, J.S.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2229
Polymers10,8676
Non-polymers3553
Water68538
1
A: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules

A: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,44418
Polymers21,73512
Non-polymers7096
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
Unit cell
Length a, b, c (Å)57.831, 57.831, 61.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein/peptide
ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL


Mass: 1811.216 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5, 47% (v/v) 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.079→38.9 Å / Num. obs: 13934 / % possible obs: 99.9 % / Redundancy: 24.8 % / CC1/2: 0.993 / Net I/σ(I): 78.3
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 27.9 / Num. unique obs: 577 / CC1/2: 0.998 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.079→28.916 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 745 9.81 %
Rwork0.1718 --
obs0.176 13934 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.079→28.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 24 38 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008798
X-RAY DIFFRACTIONf_angle_d1.5661060
X-RAY DIFFRACTIONf_dihedral_angle_d30.282543
X-RAY DIFFRACTIONf_chiral_restr0.23125
X-RAY DIFFRACTIONf_plane_restr0.005121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0792-2.15350.29111410.19811260X-RAY DIFFRACTION99
2.1535-2.23970.24681360.18651265X-RAY DIFFRACTION100
2.2397-2.34160.2271400.16291254X-RAY DIFFRACTION100
2.3416-2.4650.25241380.16571243X-RAY DIFFRACTION100
2.465-2.61930.22641370.1691269X-RAY DIFFRACTION100
2.6193-2.82140.20221390.18381237X-RAY DIFFRACTION100
2.8214-3.10510.22971350.16951263X-RAY DIFFRACTION100
3.1051-3.55370.21321380.16471255X-RAY DIFFRACTION100
3.5537-4.47460.16761470.14991251X-RAY DIFFRACTION100
4.4746-28.91830.22171160.18911270X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5701-4.5213-2.61368.41534.15536.9656-0.0355-0.1203-0.21130.53940.2979-0.72420.48480.6299-0.08310.2360.0107-0.06410.2152-0.03980.318340.22462.24830.5631
23.94312.7728-4.11155.6826-2.93954.93690.1851-0.17410.3090.06840.05610.06080.11660.2542-0.28480.2039-0.0319-0.0270.2304-0.00730.191429.938211.596427.7735
35.3147-3.16753.95298.5153-1.14534.57330.24280.4267-0.1694-0.4826-0.0537-0.3307-0.49270.5336-0.09980.2048-0.02850.04810.2782-0.01630.251540.94629.239818.3264
44.86713.5715.95934.05724.14527.46370.049-0.377-0.12530.0682-0.25140.2778-0.1844-0.40980.11490.2210.0194-0.00520.21440.01540.203520.09129.576218.6688
54.2952-2.24462.08444.5835-3.77243.3721-0.0797-0.29230.17061.18160.15850.3371-0.4192-0.38280.10110.3397-0.02520.01930.23330.02340.279820.55652.119930.3632
63.78032.9063-3.85843.4385-3.31276.32870.22670.43560.24-0.0891-0.22990.1856-0.84020.2264-0.02790.3713-0.0698-0.04750.24990.02860.216335.878122.827729.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' 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