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

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Basic information

Entry
Database: PDB / ID: 7nfh
TitleA heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(MaId)4.
ComponentsCC-Type2-(MaId)4
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRhys, 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: Data collection / Database references / Category: citation / citation_author / diffrn
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 / _diffrn.ambient_temp
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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-(MaId)4
B: CC-Type2-(MaId)4
C: CC-Type2-(MaId)4
D: CC-Type2-(MaId)4
E: CC-Type2-(MaId)4
F: CC-Type2-(MaId)4
G: CC-Type2-(MaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,12512
Polymers23,1497
Non-polymers9765
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-128 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.920, 77.920, 100.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-106-

HOH

21D-214-

HOH

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Components

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


Mass: 3307.023 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.79 Å3/Da / Density % sol: 67.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 250 mM ammonium sulfate and 50 mM 2-morpholinoethanesulfonic acid (MES).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.62→55.94 Å / Num. obs: 45086 / % possible obs: 99.7 % / Redundancy: 19.4 % / Biso Wilson estimate: 25.77 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.025 / Rrim(I) all: 0.109 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 17.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
1.62-1.664.135132970.4890.8391.0284.26399.1
7.24-55.940.02675.959610.0070.02799.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
XDSNov 1, 2016data reduction
Aimless0.5.31data scaling
xia20.5.170-g7abc92b-dials-1.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.62→55.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.7 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 2188 4.9 %RANDOM
Rwork0.1877 ---
obs0.1907 42856 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.16 Å2 / Biso mean: 33.413 Å2 / Biso min: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å2-1.36 Å2-0 Å2
2---2.71 Å20 Å2
3---8.79 Å2
Refinement stepCycle: final / Resolution: 1.62→55.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 144 94 1790
Biso mean--62.46 45.82 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131867
X-RAY DIFFRACTIONr_bond_other_d0.0050.0181942
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.6322509
X-RAY DIFFRACTIONr_angle_other_deg1.511.5764572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4625254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78125.84759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66515391
X-RAY DIFFRACTIONr_chiral_restr0.0840.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
X-RAY DIFFRACTIONr_rigid_bond_restr4.75733809
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 175 -
Rwork0.435 3123 -
all-3298 -
obs--99.16 %

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