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

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Basic information

Entry
Database: PDB / ID: 7nfn
TitleA heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L21N-I24N.
ComponentsCC-Type2-(LaId)4-L21N-I24N
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Function / homologyHEXANE-1,6-DIOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Nov 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

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Assembly

Deposited unit
A: CC-Type2-(LaId)4-L21N-I24N
B: CC-Type2-(LaId)4-L21N-I24N
C: CC-Type2-(LaId)4-L21N-I24N
D: CC-Type2-(LaId)4-L21N-I24N
E: CC-Type2-(LaId)4-L21N-I24N
F: CC-Type2-(LaId)4-L21N-I24N
G: CC-Type2-(LaId)4-L21N-I24N
H: CC-Type2-(LaId)4-L21N-I24N
I: CC-Type2-(LaId)4-L21N-I24N
J: CC-Type2-(LaId)4-L21N-I24N
K: CC-Type2-(LaId)4-L21N-I24N
L: CC-Type2-(LaId)4-L21N-I24N
M: CC-Type2-(LaId)4-L21N-I24N
N: CC-Type2-(LaId)4-L21N-I24N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,74021
Polymers46,91314
Non-polymers8277
Water6,810378
1
A: CC-Type2-(LaId)4-L21N-I24N
B: CC-Type2-(LaId)4-L21N-I24N
C: CC-Type2-(LaId)4-L21N-I24N
D: CC-Type2-(LaId)4-L21N-I24N
E: CC-Type2-(LaId)4-L21N-I24N
F: CC-Type2-(LaId)4-L21N-I24N
G: CC-Type2-(LaId)4-L21N-I24N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,04712
Polymers23,4567
Non-polymers5915
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-82 kcal/mol
Surface area10790 Å2
MethodPISA
2
H: CC-Type2-(LaId)4-L21N-I24N
I: CC-Type2-(LaId)4-L21N-I24N
J: CC-Type2-(LaId)4-L21N-I24N
K: CC-Type2-(LaId)4-L21N-I24N
L: CC-Type2-(LaId)4-L21N-I24N
M: CC-Type2-(LaId)4-L21N-I24N
N: CC-Type2-(LaId)4-L21N-I24N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6939
Polymers23,4567
Non-polymers2362
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-89 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.898, 47.910, 62.277
Angle α, β, γ (deg.)67.390, 67.490, 77.730
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
CC-Type2-(LaId)4-L21N-I24N


Mass: 3350.919 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM magnesium chloride hexahydrate, 50 mM 2-amino-2-(hydroxymethyl)propane-1,3-diol (TRIS) and 1.7 M 1,6-hexanediol.

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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: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→44.16 Å / Num. obs: 79988 / % possible obs: 95.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.4730.6431.635110.7150.440.78386.6
7.94-44.163.60.02924.15020.9980.0190.03599.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
DIALS2.2.5-g89235367c-releasedata reduction
Aimless0.7.4data scaling
xia20.6.467-geb301d90-dials-2.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.45→44.16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.57 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 3975 5 %RANDOM
Rwork0.1338 ---
obs0.1359 75966 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.29 Å2 / Biso mean: 21.324 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.45 Å2-0.01 Å2
2--1.51 Å2-0.65 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 1.45→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 56 378 3666
Biso mean--43.44 35.51 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183813
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6574905
X-RAY DIFFRACTIONr_angle_other_deg1.5951.5938710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7265470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18919.271247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12615716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3561554
X-RAY DIFFRACTIONr_chiral_restr0.0980.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024312
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02908
X-RAY DIFFRACTIONr_rigid_bond_restr2.98837477
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 311 -
Rwork0.228 5153 -
all-5464 -
obs--88.59 %

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