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- PDB-6yb0: Crystal structure of a parallel hexameric coiled coil CC-Type2-(TaSd)2 -

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Basic information

Entry
Database: PDB / ID: 6yb0
TitleCrystal structure of a parallel hexameric coiled coil CC-Type2-(TaSd)2
ComponentsCC-Type2-(TaSd)2
KeywordsDE NOVO PROTEIN / alpha-helical barrel / de novo peptide / coiled coil / designed peptide / designed protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsScott, A.J. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council (ERC)340764 United Kingdom
European Research Council (ERC)787173 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J009784/1 United Kingdom
CitationJournal: Nat.Chem. / Year: 2021
Title: Constructing ion channels from water-soluble alpha-helical barrels.
Authors: Scott, A.J. / Niitsu, A. / Kratochvil, H.T. / Lang, E.J.M. / Sengel, J.T. / Dawson, W.M. / Mahendran, K.R. / Mravic, M. / Thomson, A.R. / Brady, R.L. / Liu, L. / Mulholland, A.J. / Bayley, H. ...Authors: Scott, A.J. / Niitsu, A. / Kratochvil, H.T. / Lang, E.J.M. / Sengel, J.T. / Dawson, W.M. / Mahendran, K.R. / Mravic, M. / Thomson, A.R. / Brady, R.L. / Liu, L. / Mulholland, A.J. / Bayley, H. / DeGrado, W.F. / Wallace, M.I. / Woolfson, D.N.
History
DepositionMar 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(TaSd)2
B: CC-Type2-(TaSd)2
C: CC-Type2-(TaSd)2
D: CC-Type2-(TaSd)2
E: CC-Type2-(TaSd)2
F: CC-Type2-(TaSd)2
G: CC-Type2-(TaSd)2
H: CC-Type2-(TaSd)2
I: CC-Type2-(TaSd)2
J: CC-Type2-(TaSd)2
K: CC-Type2-(TaSd)2
L: CC-Type2-(TaSd)2


Theoretical massNumber of molelcules
Total (without water)46,96212
Polymers46,96212
Non-polymers00
Water5,332296
1
A: CC-Type2-(TaSd)2
B: CC-Type2-(TaSd)2
C: CC-Type2-(TaSd)2
D: CC-Type2-(TaSd)2
E: CC-Type2-(TaSd)2
F: CC-Type2-(TaSd)2


Theoretical massNumber of molelcules
Total (without water)23,4816
Polymers23,4816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-97 kcal/mol
Surface area11230 Å2
MethodPISA
2
G: CC-Type2-(TaSd)2
H: CC-Type2-(TaSd)2
I: CC-Type2-(TaSd)2
J: CC-Type2-(TaSd)2
K: CC-Type2-(TaSd)2
L: CC-Type2-(TaSd)2


Theoretical massNumber of molelcules
Total (without water)23,4816
Polymers23,4816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-95 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.404, 81.566, 90.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 25 or resid 27 through 36))
21(chain B and (resid 1 through 25 or resid 27 through 36))
31(chain C and (resid 1 through 25 or resid 27 through 36))
41(chain D and (resid 1 through 25 or resid 27 through 36))
51(chain E and (resid 1 through 25 or resid 27 through 36))
61(chain F and (resid 1 through 25 or resid 27 through 36))
71(chain G and (resid 1 through 25 or resid 27 through 36))
81(chain H and (resid 1 through 25 or resid 27 through 36))
91(chain I and (resid 1 through 25 or resid 27 through 36))
101(chain J and (resid 1 through 25 or resid 27 through 36))
111(chain K and (resid 1 through 25 or resid 27 through 36))
121(chain L and (resid 1 through 25 or resid 27 through 36))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALA(chain A and (resid 1 through 25 or resid 27 through 36))AA1 - 252 - 26
12ALAALALYSLYS(chain A and (resid 1 through 25 or resid 27 through 36))AA27 - 3628 - 37
21GLYGLYALAALA(chain B and (resid 1 through 25 or resid 27 through 36))BB1 - 252 - 26
22ALAALALYSLYS(chain B and (resid 1 through 25 or resid 27 through 36))BB27 - 3628 - 37
31GLYGLYALAALA(chain C and (resid 1 through 25 or resid 27 through 36))CC1 - 252 - 26
32ALAALALYSLYS(chain C and (resid 1 through 25 or resid 27 through 36))CC27 - 3628 - 37
41GLYGLYALAALA(chain D and (resid 1 through 25 or resid 27 through 36))DD1 - 252 - 26
42ALAALALYSLYS(chain D and (resid 1 through 25 or resid 27 through 36))DD27 - 3628 - 37
51GLYGLYALAALA(chain E and (resid 1 through 25 or resid 27 through 36))EE1 - 252 - 26
52ALAALALYSLYS(chain E and (resid 1 through 25 or resid 27 through 36))EE27 - 3628 - 37
61GLYGLYALAALA(chain F and (resid 1 through 25 or resid 27 through 36))FF1 - 252 - 26
62ALAALALYSLYS(chain F and (resid 1 through 25 or resid 27 through 36))FF27 - 3628 - 37
71GLYGLYALAALA(chain G and (resid 1 through 25 or resid 27 through 36))GG1 - 252 - 26
72ALAALALYSLYS(chain G and (resid 1 through 25 or resid 27 through 36))GG27 - 3628 - 37
81GLYGLYALAALA(chain H and (resid 1 through 25 or resid 27 through 36))HH1 - 252 - 26
82ALAALALYSLYS(chain H and (resid 1 through 25 or resid 27 through 36))HH27 - 3628 - 37
91GLYGLYALAALA(chain I and (resid 1 through 25 or resid 27 through 36))II1 - 252 - 26
92ALAALALYSLYS(chain I and (resid 1 through 25 or resid 27 through 36))II27 - 3628 - 37
101GLYGLYALAALA(chain J and (resid 1 through 25 or resid 27 through 36))JJ1 - 252 - 26
102ALAALALYSLYS(chain J and (resid 1 through 25 or resid 27 through 36))JJ27 - 3628 - 37
111GLYGLYALAALA(chain K and (resid 1 through 25 or resid 27 through 36))KK1 - 252 - 26
112ALAALALYSLYS(chain K and (resid 1 through 25 or resid 27 through 36))KK27 - 3628 - 37
121GLYGLYALAALA(chain L and (resid 1 through 25 or resid 27 through 36))LL1 - 252 - 26
122ALAALALYSLYS(chain L and (resid 1 through 25 or resid 27 through 36))LL27 - 3628 - 37

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Components

#1: Protein/peptide
CC-Type2-(TaSd)2


Mass: 3913.496 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.5 M NaCl, 0.05 M BIS-Tris

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91974 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91974 Å / Relative weight: 1
ReflectionResolution: 1.86→81.6 Å / Num. obs: 48308 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Net I/σ(I): 10.6
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2272 / CC1/2: 0.431 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Parametric Model

Resolution: 1.86→60.63 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.2281 2311 4.8 %
Rwork0.1895 --
obs0.1912 48192 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.48 Å2 / Biso mean: 44.002 Å2 / Biso min: 20.14 Å2
Refinement stepCycle: final / Resolution: 1.86→60.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 296 3552
Biso mean---49.02 -
Num. residues----442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1936X-RAY DIFFRACTION7.074TORSIONAL
12B1936X-RAY DIFFRACTION7.074TORSIONAL
13C1936X-RAY DIFFRACTION7.074TORSIONAL
14D1936X-RAY DIFFRACTION7.074TORSIONAL
15E1936X-RAY DIFFRACTION7.074TORSIONAL
16F1936X-RAY DIFFRACTION7.074TORSIONAL
17G1936X-RAY DIFFRACTION7.074TORSIONAL
18H1936X-RAY DIFFRACTION7.074TORSIONAL
19I1936X-RAY DIFFRACTION7.074TORSIONAL
110J1936X-RAY DIFFRACTION7.074TORSIONAL
111K1936X-RAY DIFFRACTION7.074TORSIONAL
112L1936X-RAY DIFFRACTION7.074TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.90.41521280.34382575270396
1.9-1.940.32211420.301226402782100
1.94-1.980.30231470.26626382785100
1.98-2.030.26371280.223526892817100
2.03-2.090.20491410.209226512792100
2.09-2.150.25661420.209826842826100
2.15-2.220.21731230.195926842807100
2.22-2.30.21211560.18826452801100
2.3-2.390.22621570.192526812838100
2.39-2.50.24861390.192526652804100
2.5-2.630.16381280.161327282856100
2.63-2.790.20411250.167427052830100
2.79-3.010.20931120.185327502862100
3.01-3.310.22251390.177227192858100
3.31-3.790.19971530.182927292882100
3.79-4.780.21061190.160427932912100
4.78-60.630.28931320.209929053037100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.90020.7232.22833.18031.86155.04440.09090.2885-0.24150.10550.1788-0.02820.33750.3059-0.34010.22290.0040.0260.19040.00680.226286.275879.693197.1402
24.21131.98842.94853.1252.72255.4132-0.21050.4775-0.0404-0.32060.1790.142-0.20580.265-0.09110.2715-0.02330.00290.27220.01590.245487.376484.682590.5769
34.27762.41591.61294.16461.85273.905-0.39590.38750.3667-0.71520.08110.4885-0.4548-0.03650.27880.34030.0272-0.04160.24020.0210.275482.800291.222789.7587
45.1462.7892.57984.5482.39644.3619-0.0307-0.33910.1525-0.5303-0.38340.4938-0.276-0.53450.48410.25840.0709-0.04890.2575-0.04040.322976.272892.226894.5846
52.08861.62171.16344.10232.75863.8530.1145-0.0960.09630.3231-0.41310.60180.3564-0.53510.31960.2259-0.0190.01740.2863-0.05530.375274.749986.9304100.5223
62.0112.21972.05345.09122.23154.44130.2157-0.0775-0.27580.4115-0.1518-0.00380.596-0.45080.01050.2169-0.04070.04490.26440.00090.312479.78580.3571101.6359
74.3833-2.21842.7414.5214-1.94254.702-0.5138-0.44690.20460.4340.24740.0515-0.6993-0.35370.32520.31660.0051-0.00620.2562-0.03730.2648101.667101.767879.1815
83.9021-1.6261.74053.1705-2.24584.2496-0.0541-0.2787-0.21510.14110.23220.3299-0.3652-0.4593-0.09030.24710.02620.0210.2289-0.03670.199495.675896.747880.3943
93.0897-0.60982.03843.264-2.623.82220.1999-0.0804-0.1181-0.36850.04150.32720.4172-0.3953-0.2650.24340.02080.00250.2698-0.0380.221394.613290.470574.7515
103.0682-1.96072.15824.4675-2.21764.10730.17680.24150.0524-0.6332-0.2684-0.0830.48320.1732-0.02680.26930.007-0.00450.2501-0.04320.232699.963989.534568.7027
114.371-1.4621.48474.7261-2.35144.41050.01280.49070.2332-0.2315-0.3859-0.45750.03240.51620.34690.1921-0.01120.01720.2509-0.03180.2051106.32794.521568.1298
124.7003-1.26322.23265.0609-2.68594.3825-0.16550.18960.6825-0.0144-0.2232-0.4268-0.31870.06790.43950.2125-0.0263-0.01780.2035-0.02190.2433106.8808100.838773.1277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )A1 - 37
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 36 )B1 - 36
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 37 )C1 - 37
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 37 )D1 - 37
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 37 )E1 - 37
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 36 )F1 - 36
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 37 )G1 - 37
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 37 )H1 - 37
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 37 )I1 - 37
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 37 )J1 - 37
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 37 )K1 - 37
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 37 )L1 - 37

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