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- PDB-6yb2: Crystal structure of a parallel hexameric coiled coil CC-Type2-(TaId)2 -

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Basic information

Entry
Database: PDB / ID: 6yb2
TitleCrystal structure of a parallel hexameric coiled coil CC-Type2-(TaId)2
ComponentsCC-Type2-(TaId)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: 1.18 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(TaId)2
B: CC-Type2-(TaId)2
C: CC-Type2-(TaId)2
D: CC-Type2-(TaId)2
E: CC-Type2-(TaId)2
F: CC-Type2-(TaId)2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4498
Polymers19,2656
Non-polymers1842
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-105 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.010, 55.990, 90.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 8 or (resid 9...
21(chain B and (resid 1 through 8 or (resid 9...
31(chain C and (resid 1 through 7 or (resid 8...
41(chain D and (resid 1 through 7 or (resid 8...
51(chain E and (resid 1 through 8 or (resid 9...
61(chain F and (resid 1 through 7 or (resid 8...

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
11GLYGLYLYSLYS(chain A and (resid 1 through 8 or (resid 9...AA1 - 82 - 9
12GLUGLUGLUGLU(chain A and (resid 1 through 8 or (resid 9...AA910
13ACEACENH2NH2(chain A and (resid 1 through 8 or (resid 9...AA0 - 311 - 32
14ACEACENH2NH2(chain A and (resid 1 through 8 or (resid 9...AA0 - 311 - 32
21GLYGLYLYSLYS(chain B and (resid 1 through 8 or (resid 9...BB1 - 82 - 9
22GLUGLUGLUGLU(chain B and (resid 1 through 8 or (resid 9...BB910
23ACEACENH2NH2(chain B and (resid 1 through 8 or (resid 9...BB0 - 311 - 32
24ACEACENH2NH2(chain B and (resid 1 through 8 or (resid 9...BB0 - 311 - 32
31GLYGLYLEULEU(chain C and (resid 1 through 7 or (resid 8...CC1 - 72 - 8
32LYSLYSLYSLYS(chain C and (resid 1 through 7 or (resid 8...CC89
33ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
34ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
35ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
36ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
37ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
38ACEACENH2NH2(chain C and (resid 1 through 7 or (resid 8...CC0 - 311 - 32
41GLYGLYLEULEU(chain D and (resid 1 through 7 or (resid 8...DD1 - 72 - 8
42LYSLYSLYSLYS(chain D and (resid 1 through 7 or (resid 8...DD89
43ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
44ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
45ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
46ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
47ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
48ACEACENH2NH2(chain D and (resid 1 through 7 or (resid 8...DD0 - 311 - 32
51GLYGLYLYSLYS(chain E and (resid 1 through 8 or (resid 9...EE1 - 82 - 9
52GLUGLUGLUGLU(chain E and (resid 1 through 8 or (resid 9...EE910
53ACEACENH2NH2(chain E and (resid 1 through 8 or (resid 9...EE0 - 311 - 32
54ACEACENH2NH2(chain E and (resid 1 through 8 or (resid 9...EE0 - 311 - 32
61GLYGLYLEULEU(chain F and (resid 1 through 7 or (resid 8...FF1 - 72 - 8
62LYSLYSLYSLYS(chain F and (resid 1 through 7 or (resid 8...FF89
63ACEACENH2NH2(chain F and (resid 1 through 7 or (resid 8...FF0 - 311 - 32
64ACEACENH2NH2(chain F and (resid 1 through 7 or (resid 8...FF0 - 311 - 32
65ACEACENH2NH2(chain F and (resid 1 through 7 or (resid 8...FF0 - 311 - 32
66ACEACENH2NH2(chain F and (resid 1 through 7 or (resid 8...FF0 - 311 - 32
67ACEACENH2NH2(chain F and (resid 1 through 7 or (resid 8...FF0 - 311 - 32

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Components

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


Mass: 3210.763 Da / Num. of mol.: 6 / 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.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, 40% v/v MPD

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.94999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94999 Å / Relative weight: 1
ReflectionResolution: 1.18→23.817 Å / Num. obs: 52714 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 17.1047993446 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0707 / Net I/σ(I): 12.8
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 1.69 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21633 / CC1/2: 0.631 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Parametric Model

Resolution: 1.18→23.8166039108 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.36
RfactorNum. reflection% reflection
Rfree0.1911 2610 4.96 %
Rwork0.1593 --
obs0.1609 52639 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 290.66 Å2 / Biso mean: 29.3903 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 1.18→23.8166039108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 28 141 1513
Biso mean--77 42.11 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081477
X-RAY DIFFRACTIONf_angle_d0.8762009
X-RAY DIFFRACTIONf_chiral_restr0.057242
X-RAY DIFFRACTIONf_plane_restr0.005248
X-RAY DIFFRACTIONf_dihedral_angle_d19.101547
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A575X-RAY DIFFRACTION14.242TORSIONAL
12B575X-RAY DIFFRACTION14.242TORSIONAL
13C575X-RAY DIFFRACTION14.242TORSIONAL
14D575X-RAY DIFFRACTION14.242TORSIONAL
15E575X-RAY DIFFRACTION14.242TORSIONAL
16F575X-RAY DIFFRACTION14.242TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.18-1.20150.35651380.3474254999
1.2015-1.22460.3581140.3224260599
1.2246-1.24960.33321500.3024257199
1.2496-1.27680.2911380.262596100
1.2768-1.30650.27821350.23032620100
1.3065-1.33910.24971190.2022613100
1.3391-1.37530.20821130.17392615100
1.3753-1.41580.19281420.15092636100
1.4158-1.46150.18411370.1492585100
1.4615-1.51370.17851410.1491256198
1.5137-1.57430.19891310.13442627100
1.5743-1.64590.16121310.12172665100
1.6459-1.73270.16061490.12082626100
1.7327-1.84120.17781360.14412637100
1.8412-1.98330.21111450.14882623100
1.9833-2.18280.17961450.13652662100
2.1828-2.49830.17131570.13992667100
2.4983-3.14650.17781290.14832739100
3.1465-23.81660391080.19151600.17352832100

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