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- PDB-7nfp: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -

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Basic information

Entry
Database: PDB / ID: 7nfp
TitleA heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I17K
ComponentsCC-Type2-(LaId)4-I17K
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsBurton, A.J. / Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Differential sensing with arrays of de novo designed peptide assemblies.
Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. ...Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. / Brady, R.L. / Tew, D. / Wood, C.W. / Woolfson, D.N.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(LaId)4-I17K
B: CC-Type2-(LaId)4-I17K
C: CC-Type2-(LaId)4-I17K
D: CC-Type2-(LaId)4-I17K
E: CC-Type2-(LaId)4-I17K
F: CC-Type2-(LaId)4-I17K
G: CC-Type2-(LaId)4-I17K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0339
Polymers23,8487
Non-polymers1842
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-100 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.180, 130.720, 61.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide
CC-Type2-(LaId)4-I17K


Mass: 3406.903 Da / Num. of mol.: 7 / 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.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.1 M NaCl, 10% v/v 2-propanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.43→44.67 Å / Num. obs: 46158 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.047 / Net I/σ(I): 10.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2238 / CC1/2: 0.8 / Rpim(I) all: 0.437 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.43→44.665 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 2294 4.99 %
Rwork0.1564 --
obs0.1579 46009 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→44.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 12 223 1880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051676
X-RAY DIFFRACTIONf_angle_d0.7312211
X-RAY DIFFRACTIONf_dihedral_angle_d3.481842
X-RAY DIFFRACTIONf_chiral_restr0.041248
X-RAY DIFFRACTIONf_plane_restr0.003277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.46110.26121310.2072650X-RAY DIFFRACTION98
1.4611-1.49510.23831470.17532664X-RAY DIFFRACTION98
1.4951-1.53250.19021270.14582707X-RAY DIFFRACTION98
1.5325-1.57390.19721370.13962720X-RAY DIFFRACTION100
1.5739-1.62020.17731500.1432702X-RAY DIFFRACTION100
1.6202-1.67250.18951490.13872728X-RAY DIFFRACTION100
1.6725-1.73230.16681340.13712733X-RAY DIFFRACTION100
1.7323-1.80170.16551490.14012707X-RAY DIFFRACTION100
1.8017-1.88370.17641470.13282704X-RAY DIFFRACTION100
1.8837-1.9830.14841480.13362751X-RAY DIFFRACTION99
1.983-2.10720.18741740.14942711X-RAY DIFFRACTION100
2.1072-2.26990.15311460.12872735X-RAY DIFFRACTION99
2.2699-2.49830.19821400.15472764X-RAY DIFFRACTION99
2.4983-2.85980.19941390.15562766X-RAY DIFFRACTION100
2.8598-3.60280.19511370.16152799X-RAY DIFFRACTION99
3.6028-44.6650.19021390.19042874X-RAY DIFFRACTION98

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