[English] 日本語
Yorodumi
- PDB-6q5r: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q5r
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-LL-KgEb
ComponentsCC-Hex*-LL-KgEb
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / cc-hex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsBeesley, J.L. / Rhys, G.G. / Wood, C.W. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, Belgium, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 Belgium
Biotechnology and Biological Sciences Research CouncilBB/R00661X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K03927X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles.
Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Hex*-LL-KgEb
B: CC-Hex*-LL-KgEb
C: CC-Hex*-LL-KgEb
D: CC-Hex*-LL-KgEb
E: CC-Hex*-LL-KgEb
F: CC-Hex*-LL-KgEb
G: CC-Hex*-LL-KgEb
H: CC-Hex*-LL-KgEb
I: CC-Hex*-LL-KgEb
J: CC-Hex*-LL-KgEb
K: CC-Hex*-LL-KgEb
L: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00314
Polymers38,81812
Non-polymers1842
Water4,972276
1
A: CC-Hex*-LL-KgEb
B: CC-Hex*-LL-KgEb
C: CC-Hex*-LL-KgEb
D: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,9394
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-65 kcal/mol
Surface area6920 Å2
MethodPISA
2
E: CC-Hex*-LL-KgEb
F: CC-Hex*-LL-KgEb
G: CC-Hex*-LL-KgEb
H: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,9394
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-65 kcal/mol
Surface area6870 Å2
MethodPISA
3
I: CC-Hex*-LL-KgEb
J: CC-Hex*-LL-KgEb
K: CC-Hex*-LL-KgEb
L: CC-Hex*-LL-KgEb


Theoretical massNumber of molelcules
Total (without water)12,9394
Polymers12,9394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-65 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.626, 46.748, 48.162
Angle α, β, γ (deg.)88.70, 61.70, 81.67
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide
CC-Hex*-LL-KgEb


Mass: 3234.871 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.63 M ammonium sulfate, 0.1 M lithium sulfate, 50 mM Tris

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.61→42.34 Å / Num. obs: 43409 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.89 Å2 / CC1/2: 0.945 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.173 / Rrim(I) all: 0.244 / Χ2: 0.75 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.61-1.650.9872.631300.5030.9871.3960.695.4
7.2-42.340.2368.85000.9270.2360.3342.2899.2

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALS1.10.3data reduction
Aimless0.5.32data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→39.974 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 2076 4.79 %RANDOM
Rwork0.1958 ---
obs0.1977 43308 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→39.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 12 276 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052884
X-RAY DIFFRACTIONf_angle_d0.7773866
X-RAY DIFFRACTIONf_dihedral_angle_d1.7172321
X-RAY DIFFRACTIONf_chiral_restr0.031461
X-RAY DIFFRACTIONf_plane_restr0.004470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.64740.28051270.21782551X-RAY DIFFRACTION91
1.6474-1.68860.25161440.22452699X-RAY DIFFRACTION95
1.6886-1.73430.25461470.22822718X-RAY DIFFRACTION95
1.7343-1.78530.2761290.22392736X-RAY DIFFRACTION96
1.7853-1.8430.25931380.21832713X-RAY DIFFRACTION96
1.843-1.90880.2321410.19872725X-RAY DIFFRACTION96
1.9088-1.98520.23491500.20272753X-RAY DIFFRACTION97
1.9852-2.07560.26381330.19282790X-RAY DIFFRACTION97
2.0756-2.1850.22111500.1852760X-RAY DIFFRACTION97
2.185-2.32190.24091500.19072739X-RAY DIFFRACTION97
2.3219-2.50120.23441390.19182784X-RAY DIFFRACTION98
2.5012-2.75280.21021430.1812805X-RAY DIFFRACTION98
2.7528-3.1510.23511430.1972790X-RAY DIFFRACTION98
3.151-3.96940.19371010.17872857X-RAY DIFFRACTION99
3.9694-39.98580.26071410.20292812X-RAY DIFFRACTION99
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)
11.2289-1.7227-1.39796.33684.32944.39-0.05350.04170.02620.30230.2823-0.7030.16660.1062-0.1110.0683-0.0135-0.0150.13230.01440.1892.7556-3.9662-0.7364
21.29821.2670.03165.34941.20811.5554-0.10170.09070.0338-0.1431-0.00510.7364-0.0979-0.02860.1020.0471-0.0097-0.00950.12290.01410.1387-10.8748-2.4259-1.1214
32.4117-2.2948-1.18255.54512.43272.01440.0160.02020.03730.6816-0.0389-0.35030.06420.0138-0.04560.0823-0.02770.0060.10370.02520.0708-6.497-2.34795.9314
41.79591.44290.2274.01241.30361.3948-0.18670.2556-0.098-0.71670.4954-0.9577-0.21530.1203-0.07790.1578-0.03510.06290.11830.03380.1266-1.5491.1089-5.9484
52.82731.8111.40972.34022.32133.1861-0.19650.06140.0565-0.58530.28510.0158-0.19660.0719-0.10890.087-0.02320.00380.12260.0270.0999-29.4179-4.9599-8.0605
63.4546-3.9044-1.12745.27232.62593.0185-0.2715-0.3578-0.04280.57650.4421-0.31730.0910.2369-0.12590.10630.0167-0.0050.18650.03080.1279-24.177-7.85583.9481
72.19491.94181.29055.91634.31484.933-0.2508-0.02210.0422-0.46880.5429-0.4578-0.22770.439-0.1380.08330.00540.00240.14020.00640.1673-20.213-3.7778-1.5273
81.7527-1.51370.05831.83070.94721.9253-0.1420.0379-0.0589-0.10950.18040.61140.0804-0.04040.03140.0562-0.00920.00240.11030.01680.1649-33.4635-4.512-1.012
91.0989-0.0374-0.72241.242-0.83681.746-0.09910.0916-0.002-0.51990.11770.2792-0.0811-0.16930.01420.1924-0.0335-0.0270.14360.03160.0792-18.8095-2.435514.9492
100.81680.136-0.67893.79553.84044.6196-0.194-0.0311-0.0568-0.08870.3066-0.5156-0.15570.258-0.01790.2364-0.0192-0.02630.11940.04640.1368-11.1768-4.959726.1309
110.62080.153-0.01824.0944-0.85951.32120.0104-0.0552-0.0450.65210.01870.68420.0129-0.1414-0.09230.2388-0.03120.03050.13190.03510.0829-18.7502-7.578925.0529
120.70810.29581.28832.98912.67613.61230.0265-0.0086-0.0775-0.19510.07-0.5825-0.026-0.0874-0.09720.2097-0.04740.06580.10530.00930.1047-11.0501-4.975814.2658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:30)
2X-RAY DIFFRACTION2(chain B and resseq 1:30)
3X-RAY DIFFRACTION3(chain C and resseq 1:30)
4X-RAY DIFFRACTION4(chain D and resseq 1:30)
5X-RAY DIFFRACTION5(chain E and resseq 1:30)
6X-RAY DIFFRACTION6(chain F and resseq 1:30)
7X-RAY DIFFRACTION7(chain G and resseq 1:30)
8X-RAY DIFFRACTION8(chain H and resseq 1:30)
9X-RAY DIFFRACTION9(chain I and resseq 1:30)
10X-RAY DIFFRACTION10(chain J and resseq 1:30)
11X-RAY DIFFRACTION11(chain K and resseq 1:30)
12X-RAY DIFFRACTION12(chain L and resseq 1:30)

+
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