[English] 日本語
Yorodumi
- PDB-6g6e: Crystal structure of a parallel seven-helix coiled coil CC-Type2-deLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g6e
TitleCrystal structure of a parallel seven-helix coiled coil CC-Type2-deLI
ComponentsCC-Type2-deLI
KeywordsDE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
Authors: Rhys, G.G. / Wood, C.W. / Lang, E.J.M. / Mulholland, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-deLI
B: CC-Type2-deLI
C: CC-Type2-deLI
D: CC-Type2-deLI
E: CC-Type2-deLI
F: CC-Type2-deLI
G: CC-Type2-deLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,04812
Polymers22,5887
Non-polymers4605
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-81 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.201, 47.950, 129.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11G-101-

HOH

-
Components

#1: Protein/peptide
CC-Type2-deLI


Mass: 3226.807 Da / Num. of mol.: 7 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.93 Å3/Da / Density % sol: 36.22 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Magnesium Chloride hexahydrate, 50 mM Sodium HEPES and 15% w/v PEG 400

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.26→64.67 Å / Num. obs: 65209 / % possible obs: 99.9 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.02 / Rrim(I) all: 0.067 / Net I/σ(I): 15.5 / Num. measured all: 746680 / Scaling rejects: 239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.26-1.289.91.11931760.8350.3691.1899.5
6.9-64.6710.10.074850.9930.0250.07599.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.26 Å64.67 Å
Translation1.26 Å64.67 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→64.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.086 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3271 5 %RANDOM
Rwork0.1805 ---
obs0.1815 61872 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 22.505 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---0.16 Å20 Å2
3----2.16 Å2
Refinement stepCycle: final / Resolution: 1.26→64.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 30 171 1800
Biso mean--53.28 40.87 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0181974
X-RAY DIFFRACTIONr_bond_other_d0.0030.0232176
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.8912584
X-RAY DIFFRACTIONr_angle_other_deg0.9041.9675024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4345210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.27523.37837
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36915255
X-RAY DIFFRACTIONr_chiral_restr0.1160.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 224 -
Rwork0.368 4509 -
all-4733 -
obs--99.41 %

+
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://pdbjlvh1.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