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

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Basic information

Entry
Database: PDB / ID: 8qad
TitleX-ray crystal structure of a de novo designed single-chain antiparallel 6-helix coiled-coil alpha-helical barrel, sc-apCC-6-LLIA
Componentssc-apCC-6-LLIA
KeywordsDE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.25 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-6-LLIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1902
Polymers26,6431
Non-polymers5471
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer, equilibrium centrifugation, monomer, SAXS, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-15 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.549, 60.875, 77.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein sc-apCC-6-LLIA


Mass: 26643.236 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: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium formate, 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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→47.98 Å / Num. obs: 8255 / % possible obs: 99.64 % / Redundancy: 2 % / Biso Wilson estimate: 46.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02253 / Rpim(I) all: 0.02253 / Rrim(I) all: 0.03186 / Net I/σ(I): 9.72
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.2053 / Mean I/σ(I) obs: 3 / Num. unique obs: 800 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.2053 / Rrim(I) all: 0.2903

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AutoProcessdata reduction
AutoProcessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.25→47.98 Å / SU ML: 0.2286 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.6022
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2774 373 4.53 %
Rwork0.2484 7858 -
obs0.2498 8231 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.91 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 17 3 972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001967
X-RAY DIFFRACTIONf_angle_d0.25571311
X-RAY DIFFRACTIONf_chiral_restr0.0249196
X-RAY DIFFRACTIONf_plane_restr0.0006144
X-RAY DIFFRACTIONf_dihedral_angle_d2.1551150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.580.26751250.23712544X-RAY DIFFRACTION99.78
2.58-3.240.34521180.28812594X-RAY DIFFRACTION99.6
3.24-47.980.2581300.23762720X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 18.6573636372 Å / Origin y: 26.0950926379 Å / Origin z: 15.4244710118 Å
111213212223313233
T0.292780671554 Å20.0479294333127 Å2-0.0636339796763 Å2-0.233260495711 Å2-0.0446582962865 Å2--0.378251708884 Å2
L3.22594061437 °20.556029746197 °20.563705106018 °2-6.76293793706 °2-0.667037935469 °2--4.08736587955 °2
S0.251176142042 Å °0.00764622123871 Å °-0.0848120562964 Å °0.2445300156 Å °-0.200015067034 Å °0.143173586375 Å °0.177244392337 Å °0.216935940076 Å °-0.0258676153515 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 3 through 208)

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