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- PDB-7nfl: An octameric barrel state of a de novo coiled-coil assembly: CC-T... -

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Basic information

Entry
Database: PDB / ID: 7nfl
TitleAn octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I24N.
ComponentsCC-Type2-(LaId)4-I24N
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.3Nov 13, 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-(LaId)4-I24N
B: CC-Type2-(LaId)4-I24N


Theoretical massNumber of molelcules
Total (without water)6,4722
Polymers6,4722
Non-polymers00
Water68538
1
A: CC-Type2-(LaId)4-I24N
B: CC-Type2-(LaId)4-I24N

A: CC-Type2-(LaId)4-I24N
B: CC-Type2-(LaId)4-I24N

A: CC-Type2-(LaId)4-I24N
B: CC-Type2-(LaId)4-I24N

A: CC-Type2-(LaId)4-I24N
B: CC-Type2-(LaId)4-I24N


Theoretical massNumber of molelcules
Total (without water)25,8878
Polymers25,8878
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area13340 Å2
ΔGint-117 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.465, 47.465, 127.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-115-

HOH

21A-116-

HOH

31B-115-

HOH

41B-117-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 30 / Label seq-ID: 2 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein/peptide CC-Type2-(LaId)4-I24N


Mass: 3235.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM 2-(bis(2-hydroxyethyl)amino)acetic acid (BICINE) and 5% v/v 2-methyl-2,4-pentanediol (MPD).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.44→44.51 Å / Num. obs: 13654 / % possible obs: 99.7 % / Redundancy: 24.1 % / Biso Wilson estimate: 24.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.026 / Rrim(I) all: 0.128 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.44-1.4821.19.9990.69720.5913.12914.35199.1
6.44-44.5120.70.03248.720210.0080.03499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
DIALS1.14.13-g10ecfbb15-releasedata reduction
Aimless0.7.4data scaling
xia20.5.902-gffa11588-dials-1.14data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.44→44.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.852 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 671 4.9 %RANDOM
Rwork0.179 ---
obs0.1807 12979 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.69 Å2 / Biso mean: 31.791 Å2 / Biso min: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å2-0 Å2-0 Å2
2--2.06 Å20 Å2
3----4.13 Å2
Refinement stepCycle: final / Resolution: 1.44→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 0 38 482
Biso mean---50.35 -
Num. residues----62
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013482
X-RAY DIFFRACTIONr_bond_other_d0.0010.017496
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.628654
X-RAY DIFFRACTIONr_angle_other_deg1.6461.5761142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.43567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.72526.66721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0211595
X-RAY DIFFRACTIONr_chiral_restr0.0910.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02571
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0293
X-RAY DIFFRACTIONr_rigid_bond_restr3.6773977
Refine LS restraints NCS

Ens-ID: 1 / Number: 853 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 42 -
Rwork0.425 928 -
all-970 -
obs--98.68 %

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