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- PDB-8qaa: X-ray crystal structure of a de novo designed antiparallel coiled... -

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Basic information

Entry
Database: PDB / ID: 8qaa
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil 6-helix bundle with 4 heptad repeats, antiparallel 6-helix bundle-ALIA
Componentsantiparallel 6-helix bundle-ALIA
KeywordsDE NOVO PROTEIN / COILED COIL / 6-HELIX BUNDLE / DE NOVO PROTEIN DESIGN / PEPTIDE ASSEMBLY
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 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
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: antiparallel 6-helix bundle-ALIA
B: antiparallel 6-helix bundle-ALIA
C: antiparallel 6-helix bundle-ALIA
D: antiparallel 6-helix bundle-ALIA
E: antiparallel 6-helix bundle-ALIA
F: antiparallel 6-helix bundle-ALIA


Theoretical massNumber of molelcules
Total (without water)19,4096
Polymers19,4096
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-125 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.274, 89.496, 32.667
Angle α, β, γ (deg.)90.00, 115.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
antiparallel 6-helix bundle-ALIA


Mass: 3234.871 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each NPS, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→44.75 Å / Num. obs: 19749 / % possible obs: 98.26 % / Redundancy: 7 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1184 / Rpim(I) all: 0.0493 / Rrim(I) all: 0.1285 / Net I/σ(I): 8.63
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8176 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 19709 / CC1/2: 0.783 / CC star: 0.937 / Rpim(I) all: 0.3437 / Rrim(I) all: 0.8881 / % possible all: 96.93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→44.75 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1004 5.09 %
Rwork0.1806 --
obs0.1829 19709 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 171 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061266
X-RAY DIFFRACTIONf_angle_d0.5711707
X-RAY DIFFRACTIONf_dihedral_angle_d13.819182
X-RAY DIFFRACTIONf_chiral_restr0.036216
X-RAY DIFFRACTIONf_plane_restr0.004207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.29511390.24652623X-RAY DIFFRACTION97
1.68-1.790.25951360.22522648X-RAY DIFFRACTION98
1.79-1.930.28851380.20592658X-RAY DIFFRACTION98
1.93-2.120.22571500.17842651X-RAY DIFFRACTION98
2.12-2.430.22051360.15892702X-RAY DIFFRACTION99
2.43-3.060.25041280.17012711X-RAY DIFFRACTION99
3.06-44.750.19511770.17452712X-RAY DIFFRACTION99
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)
10.92391.8682-0.41096.4613-1.5140.7154-0.04770.06990.047-0.44070.08650.2460.0779-0.0176-0.05550.2312-0.01280.01880.109700.0773-2.348519.09469.9015
22.06262.67280.72273.97470.57850.4953-0.10850.0622-0.0511-0.10740.2477-0.27430.02470.108-0.06590.23950.0140.04550.17430.00740.12468.274721.419213.9086
31.52311.8687-0.73714.2413-2.10192.2333-0.01940.05430.1842-0.15150.07630.34140.0206-0.1384-0.13550.1588-0.02760.01880.1529-0.00080.0246-5.484623.793915.6635
41.0308-0.51880.57795.7934-2.4342.3484-0.078-0.1417-0.00130.1750.24090.4381-0.0882-0.1003-0.09340.1515-0.01290.03010.1558-0.00680.0421-4.889119.829525.6161
50.6147-1.38060.14996.85-0.14940.0456-0.1137-0.11870.01050.45620.11710.0132-0.0416-0.0154-0.00490.29350.00870.00760.1819-0.00640.10181.093223.89429.9484
60.73440.75990.06122.4641-0.03110.6973-0.0322-0.0266-0.04050.16160.0231-0.45910.01210.0412-0.00250.17490.00630.0130.19470.00590.12325.772118.163821.2847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 30)
2X-RAY DIFFRACTION2(chain 'D' and resid 1 through 30)
3X-RAY DIFFRACTION3(chain 'E' and resid 0 through 30)
4X-RAY DIFFRACTION4(chain 'B' and resid 0 through 30)
5X-RAY DIFFRACTION5(chain 'C' and resid 0 through 30)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 30)

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