[English] 日本語
Yorodumi
- PDB-6y7n: The crystal structure of the eight-bladed symmetrical designer pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y7n
TitleThe crystal structure of the eight-bladed symmetrical designer protein Tako8 in the presence of tellurotungstic Anderson-Evans (TEW)
ComponentsTako8
KeywordsDE NOVO PROTEIN / Designer protein / polyoxometalate / POM / TEW / packing
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVandebroek, L. / Noguchi, H. / Parac-Vogt, T.N. / Van Meervelt, L. / Voet, A.R.D.
CitationJournal: Cryst.Growth Des. / Year: 2021
Title: Shape and Size Complementarity-Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters
Authors: Vandebroek, L. / Noguchi, H. / Kamata, K. / Tame, J.R.H. / Parac-Vogt, T.N. / Voet, A.R.D.
History
DepositionMar 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tako8
B: Tako8


Theoretical massNumber of molelcules
Total (without water)70,0482
Polymers70,0482
Non-polymers00
Water10,737596
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-5 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.586, 60.929, 73.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Tako8


Mass: 35024.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1M sodium acetate, 3.1M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.6→46.94 Å / Num. obs: 85806 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.023 / Rrim(I) all: 0.033 / Net I/σ(I): 21.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 4215 / CC1/2: 0.994 / Rpim(I) all: 0.07 / Rrim(I) all: 0.103

-
Processing

Software
NameVersionClassification
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6g6m

6g6m


Resolution: 1.6→46.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 37.65
RfactorNum. reflection% reflection
Rfree0.2495 4444 5.19 %
Rwork0.217 --
obs0.2188 85551 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.51 Å2 / Biso mean: 19.4706 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 1.6→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 0 596 5446
Biso mean---28.15 -
Num. residues----638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61820.35821520.26932672100
1.6182-1.63730.2851160.26712735100
1.6373-1.65720.24431340.262267799
1.6572-1.67820.23751380.23992736100
1.6782-1.70030.40081420.24872669100
1.7003-1.72360.25391340.24022714100
1.7236-1.74820.31571340.26422704100
1.7482-1.77430.29291560.24212700100
1.7743-1.8020.34211240.25632779100
1.802-1.83160.29391400.24862665100
1.8316-1.86310.25922300.23972617100
1.8631-1.8970.28011340.23332718100
1.897-1.93350.26281400.25752723100
1.9335-1.9730.23631560.22452697100
1.973-2.01590.22621400.22852694100
2.0159-2.06280.22961570.21542679100
2.0628-2.11440.27931900.21812691100
2.1144-2.17150.18151900.22412666100
2.1715-2.23540.20081540.22492669100
2.2354-2.30760.20861380.21752753100
2.3076-2.39010.2491830.22992685100
2.3901-2.48570.22971420.21732657100
2.4857-2.59890.39261160.23552752100
2.5989-2.73590.2756670.20952865100
2.7359-2.90730.31321420.21022695100
2.9073-3.13170.24291770.21592682100
3.1317-3.44670.2311810.2052711100
3.4467-3.94530.25391310.1807274199
3.9453-4.96980.20991310.173275199
4.9698-46.930.2371750.1995261093

+
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