[English] 日本語
Yorodumi
- PDB-6v5i: Coiled-coil Trimer with Ala:Leu:Ala Triad -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v5i
TitleCoiled-coil Trimer with Ala:Leu:Ala Triad
ComponentsCoiled-coil Trimer with Ala:Leu:Ala Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR15 GM116055-01 United States
CitationJournal: Biochemistry / Year: 2020
Title: Context-Dependent Stabilizing Interactions among Solvent-Exposed Residues along the Surface of a Trimeric Helix Bundle.
Authors: Stern, K.L. / Smith, M.S. / Billings, W.M. / Loftus, T.J. / Conover, B.M. / Della Corte, D. / Price, J.L.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: 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: Coiled-coil Trimer with Ala:Leu:Ala Triad
B: Coiled-coil Trimer with Ala:Leu:Ala Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7393
Polymers7,5012
Non-polymers2381
Water1,65792
1
A: Coiled-coil Trimer with Ala:Leu:Ala Triad

A: Coiled-coil Trimer with Ala:Leu:Ala Triad

A: Coiled-coil Trimer with Ala:Leu:Ala Triad


Theoretical massNumber of molelcules
Total (without water)11,2513
Polymers11,2513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3660 Å2
ΔGint-31 kcal/mol
Surface area6680 Å2
MethodPISA
2
B: Coiled-coil Trimer with Ala:Leu:Ala Triad
hetero molecules

B: Coiled-coil Trimer with Ala:Leu:Ala Triad
hetero molecules

B: Coiled-coil Trimer with Ala:Leu:Ala Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9666
Polymers11,2513
Non-polymers7153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4720 Å2
ΔGint-31 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.860, 37.860, 105.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-251-

HOH

-
Components

#1: Protein/peptide Coiled-coil Trimer with Ala:Leu:Ala Triad


Mass: 3750.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40% PEG300, 100 mM HEPES/NaOH, pH 7.5, 200 mM sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.9→31.32 Å / Num. obs: 4461 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2.0465 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1119

-
Processing

Software
NameVersionClassification
PHENIXdev_2906refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UXT

5uxt


Resolution: 1.9→31.31 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.193 753 9.93 %
Rwork0.1555 --
obs0.1593 4461 84.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.43 Å2 / Biso mean: 17.3574 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 1.9→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms528 0 16 92 636
Biso mean--27.46 24.3 -
Num. residues----68
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-2.04650.24331240.204111970
2.0465-2.25210.16041360.1559127779
2.2521-2.57690.21731540.1625140288
2.5769-3.24270.2351660.1535151693
3.2427-16.6810.16171730.1432151494

+
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