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- PDB-8qaf: X-ray crystal structure of a de novo designed single-chain antipa... -

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Basic information

Entry
Database: PDB / ID: 8qaf
TitleX-ray crystal structure of a de novo designed single-chain antiparallel 8-helix coiled-coil alpha-helical barrel, sc-apCC-8
Componentssc-apCC-8
KeywordsDE NOVO PROTEIN / coiled coil / 8-helix anti-parallel alpha-helical barrel / de novo protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2 Å
AuthorsAlbanese, K.I. / Petrenas, R. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Rationally seeded computational protein design of ɑ-helical barrels.
Authors: Albanese, K.I. / Petrenas, R. / Pirro, F. / Naudin, E.A. / Borucu, U. / Dawson, W.M. / Scott, D.A. / Leggett, G.J. / Weiner, O.D. / Oliver, T.A.A. / Woolfson, D.N.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sc-apCC-8


Theoretical massNumber of molelcules
Total (without water)9,6211
Polymers9,6211
Non-polymers00
Water25214
1
A: sc-apCC-8

A: sc-apCC-8

A: sc-apCC-8

A: sc-apCC-8


Theoretical massNumber of molelcules
Total (without water)38,4864
Polymers38,4864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area4360 Å2
ΔGint-68 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.002, 50.002, 57.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab

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Components

#1: Protein sc-apCC-8


Mass: 9621.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 33.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium formate, 0.1 M Bis Tris propane, pH 8.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→37.66 Å / Num. obs: 5290 / % possible obs: 99.62 % / Redundancy: 2 % / Biso Wilson estimate: 35.05 Å2 / CC1/2: 0.934 / CC star: 0.997 / Rmerge(I) obs: 0.01179 / Rpim(I) all: 0.01179 / Rrim(I) all: 0.01668 / Net I/σ(I): 15.06
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.09224 / Mean I/σ(I) obs: 5.24 / Num. unique obs: 504 / CC1/2: 0.976 / CC star: 0.994 / Rpim(I) all: 0.09224 / Rrim(I) all: 0.1305 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AutoProcessdata reduction
AutoProcessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2→37.66 Å / SU ML: 0.2803 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 248 4.7 %
Rwork0.2489 5023 -
obs0.2492 5271 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.25 Å2
Refinement stepCycle: LAST / Resolution: 2→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms367 0 0 14 381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063375
X-RAY DIFFRACTIONf_angle_d0.5725515
X-RAY DIFFRACTIONf_chiral_restr0.044273
X-RAY DIFFRACTIONf_plane_restr0.003560
X-RAY DIFFRACTIONf_dihedral_angle_d3.278659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.520.34341220.21132443X-RAY DIFFRACTION99.88
2.52-37.660.23221260.25892580X-RAY DIFFRACTION99.41
Refinement TLS params.Method: refined / Origin x: 44.0710997538 Å / Origin y: 16.6108111823 Å / Origin z: 12.7104009818 Å
111213212223313233
T0.203490833593 Å2-0.041992217914 Å2-0.00849056479466 Å2-0.197286896492 Å20.0175489988444 Å2--0.491430944611 Å2
L3.58663942216 °2-0.60043787746 °2-1.17784702724 °2-3.93212192614 °21.14545997046 °2--6.22622931437 °2
S-0.0207434310809 Å °-0.0665031511645 Å °-0.494434147073 Å °0.00413866319669 Å °-0.0971617362784 Å °0.362048907376 Å °-0.0041742810226 Å °-0.184123213164 Å °0.164040120549 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 0 through 64)

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