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- PDB-7nfo: A hexameric barrel state of a de novo coiled-coil assembly: CC-Ty... -

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Basic information

Entry
Database: PDB / ID: 7nfo
TitleA hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I17C.
ComponentsCC-Type2-(LaId)4-I17C
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(LaId)4-I17C
B: CC-Type2-(LaId)4-I17C
C: CC-Type2-(LaId)4-I17C


Theoretical massNumber of molelcules
Total (without water)9,6753
Polymers9,6753
Non-polymers00
Water1,11762
1
A: CC-Type2-(LaId)4-I17C
B: CC-Type2-(LaId)4-I17C
C: CC-Type2-(LaId)4-I17C

A: CC-Type2-(LaId)4-I17C
B: CC-Type2-(LaId)4-I17C
C: CC-Type2-(LaId)4-I17C


Theoretical massNumber of molelcules
Total (without water)19,3496
Polymers19,3496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8980 Å2
ΔGint-100 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.640, 43.400, 40.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-117-

HOH

21A-118-

HOH

31A-119-

HOH

41A-120-

HOH

51A-121-

HOH

61A-122-

HOH

71A-123-

HOH

81A-124-

HOH

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Components

#1: Protein/peptide CC-Type2-(LaId)4-I17C


Mass: 3224.856 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 400 mM potasium sodium tartrate tetrahydrate and 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium HEPES).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.37→40.4 Å / Num. obs: 15267 / % possible obs: 98.1 % / Redundancy: 12.3 % / Biso Wilson estimate: 18.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.37-1.417.92.370.89320.3270.8562.53383.8
6.13-40.4110.03840.520910.0120.0495.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
xia20.6.374-gccd9eb9a-dials-2.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.37→40.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.05 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 705 4.6 %RANDOM
Rwork0.1813 ---
obs0.182 14539 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.43 Å2 / Biso mean: 19.322 Å2 / Biso min: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å20 Å2
2--0.75 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 1.37→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 0 62 738
Biso mean---33.47 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013706
X-RAY DIFFRACTIONr_bond_other_d0.0010.017750
X-RAY DIFFRACTIONr_angle_refined_deg1.531.632946
X-RAY DIFFRACTIONr_angle_other_deg1.5641.5861732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.078593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.225.96226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28815146
X-RAY DIFFRACTIONr_chiral_restr0.0770.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
LS refinement shellResolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 41 -
Rwork0.343 891 -
all-932 -
obs--81.9 %

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