[English] 日本語
Yorodumi
- PDB-8a3g: X-ray crystal structure of a de novo designed antiparallel coiled... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a3g
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil homotetramer with 4 heptad repeats, apCC-Tet*
ComponentsapCC-Tet*
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / de novo protein design / peptide assembly
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.96 Å
AuthorsNaudin, E.A. / Mylemans, B. / Albanese, K.I. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V004220/1 United Kingdom
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Chem Sci / Year: 2022
Title: From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.
Authors: Naudin, E.A. / Albanese, K.I. / Smith, A.J. / Mylemans, B. / Baker, E.G. / Weiner, O.D. / Andrews, D.M. / Tigue, N. / Savery, N.J. / Woolfson, D.N.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: apCC-Tet*
B: apCC-Tet*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0084
Polymers6,9262
Non-polymers822
Water70339
1
A: apCC-Tet*
B: apCC-Tet*
hetero molecules

A: apCC-Tet*
B: apCC-Tet*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0168
Polymers13,8524
Non-polymers1644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area6540 Å2
ΔGint-72 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.015, 34.015, 87.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

-
Components

#1: Protein/peptide apCC-Tet*


Mass: 3463.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium acetate, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.96→43.77 Å / Num. obs: 31082 / % possible obs: 96.1 % / Redundancy: 20.8 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.009 / Rrim(I) all: 0.043 / Net I/σ(I): 30.3 / Num. measured all: 645142 / Scaling rejects: 144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.96-0.987.60.805843411040.7790.3010.863271.1
5.26-43.7718.60.015507127310.0040.01599.499.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
Fragonphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.96→26.86 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1687 1514 4.9 %
Rwork0.1598 29396 -
obs0.1603 30910 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.5 Å2 / Biso mean: 12.7871 Å2 / Biso min: 5.99 Å2
Refinement stepCycle: final / Resolution: 0.96→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms479 0 5 39 523
Biso mean--28.95 20.69 -
Num. residues----64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.96-0.990.20861040.22341973207773
0.99-1.030.19691180.17982331244985
1.03-1.070.15011290.13612687281697
1.07-1.120.12511470.10722692283999
1.12-1.170.12251260.10252746287299
1.17-1.250.1251480.10582719286799
1.25-1.340.12141380.113127652903100
1.34-1.480.15061400.128627922932100
1.48-1.690.14761530.13222801295499
1.69-2.130.19061550.177428603015100
2.14-26.860.19051560.19430303186100

+
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