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

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Basic information

Entry
Database: PDB / ID: 7nfk
TitleAn octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I24S.
ComponentsCC-Type2-(LaId)4-I24S
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(LaId)4-I24S
B: CC-Type2-(LaId)4-I24S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7187
Polymers6,4182
Non-polymers3005
Water97354
1
A: CC-Type2-(LaId)4-I24S
B: CC-Type2-(LaId)4-I24S
hetero molecules

A: CC-Type2-(LaId)4-I24S
B: CC-Type2-(LaId)4-I24S
hetero molecules

A: CC-Type2-(LaId)4-I24S
B: CC-Type2-(LaId)4-I24S
hetero molecules

A: CC-Type2-(LaId)4-I24S
B: CC-Type2-(LaId)4-I24S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,87228
Polymers25,6708
Non-polymers1,20220
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 area15280 Å2
ΔGint-76 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.980, 47.980, 127.820
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
11B-102-

IPA

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: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 29 / Label seq-ID: 2 - 30

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

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Components

#1: Protein/peptide CC-Type2-(LaId)4-I24S


Mass: 3208.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
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 100 mM sodium citrate tribasic dihydrate, 50 mM sodium cacodylate and 15% v/v 2-propanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / 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: 1.3→44.92 Å / Num. obs: 18806 / % possible obs: 99.5 % / Redundancy: 24.3 % / Biso Wilson estimate: 22.88 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.01 / Rrim(I) all: 0.048 / Net I/σ(I): 33.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.3-1.3320.62.6441.313640.6420.592.7199.8
5.81-44.9217.50.05782.22680.9980.0150.05999.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSNov 11, 2017data reduction
Aimless0.5.32data scaling
xia20.5.482-g030776d9-dials-1.8data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.3→44.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.634 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 986 5.2 %RANDOM
Rwork0.1848 ---
obs0.1855 17820 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.52 Å2 / Biso mean: 26.533 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.63 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 1.3→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 20 54 506
Biso mean--55.25 42.8 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013511
X-RAY DIFFRACTIONr_bond_other_d0.0010.017548
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.649688
X-RAY DIFFRACTIONr_angle_other_deg1.5711.5841262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.243570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24125.88217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11415102
X-RAY DIFFRACTIONr_chiral_restr0.0910.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0288
X-RAY DIFFRACTIONr_rigid_bond_restr2.58231058
Refine LS restraints NCS

Ens-ID: 1 / Number: 933 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 80 -
Rwork0.337 1280 -
all-1360 -
obs--99.78 %

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