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- PDB-8a09: A hexameric barrel state of a de novo coiled-coil assembly: CC-Ty... -

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Basic information

Entry
Database: PDB / ID: 8a09
TitleA hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
ComponentsA hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.35 Å
AuthorsMartin, F.J.O. / Rhys, G.G. / Dawson, W.M. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 5items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
European Research Council (ERC)787173European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 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
DepositionMay 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / 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: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
B: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2025
Polymers6,9262
Non-polymers2763
Water36020
1
A: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
B: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
hetero molecules

A: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
B: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
hetero molecules

A: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
B: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,60715
Polymers20,7786
Non-polymers8299
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11130 Å2
ΔGint-106 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.710, 53.710, 46.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

GOL

21A-101-

GOL

31A-102-

GOL

41A-201-

HOH

51A-210-

HOH

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Components

#1: Protein/peptide A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4


Mass: 3463.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.86 Å3/Da / Density % sol: 33.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 1.5 mM peptide, 50 mM Sodium acetate, 1% w/v PEG 4000 at pH 5.0
Temp details: Incubator

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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: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→32.85 Å / Num. obs: 10984 / % possible obs: 99.79 % / Redundancy: 5.2 % / Biso Wilson estimate: 20.91 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1462 / Rpim(I) all: 0.06936 / Rrim(I) all: 0.162 / Net I/σ(I): 13.01
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1089 / CC1/2: 0.529 / Rpim(I) all: 0.5337 / Rrim(I) all: 1.145 / % possible all: 99.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.35→32.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.992 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0695 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 565 5.1 %RANDOM
Rwork0.1743 ---
obs0.1753 10446 99.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 63.49 Å2 / Biso mean: 25.972 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å20 Å2
2---0.49 Å20 Å2
3---1.57 Å2
Refinement stepCycle: final / Resolution: 1.35→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms463 0 18 20 501
Biso mean--28.83 35.42 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012480
X-RAY DIFFRACTIONr_bond_other_d0.0010.016494
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.614636
X-RAY DIFFRACTIONr_angle_other_deg0.4021.5631150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.209556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2741098
X-RAY DIFFRACTIONr_chiral_restr0.0690.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0268
X-RAY DIFFRACTIONr_rigid_bond_restr3.1873974
LS refinement shellResolution: 1.35→1.383 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.342 38 -
Rwork0.317 779 -
obs--98.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.30190.4456-2.60814.5851-1.566212.20850.1212-0.0753-0.08980.0055-0.0591-0.41090.20660.4576-0.06220.01580.0125-0.01880.0243-0.01760.08217.9653-3.9043-4.1811
23.7885-0.4211-2.89852.5355-0.295313.4069-0.0358-0.0167-0.31120.11820.05180.02690.47080.1066-0.0160.03170.0034-0.02540.00430.00920.08070.5964-8.9144-4.1908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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