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

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Basic information

Entry
Database: PDB / ID: 8qag
TitleX-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 6 inner helices, sc-CC-6-95
Componentssc-CC-6-95
KeywordsDE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPetrenas, R. / Albanese, K.I. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) 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-CC-6-95
B: sc-CC-6-95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5325
Polymers67,1252
Non-polymers4063
Water724
1
A: sc-CC-6-95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8633
Polymers33,5631
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sc-CC-6-95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6692
Polymers33,5631
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.950, 88.950, 149.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein sc-CC-6-95


Mass: 33562.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 75% JCSG A6: 0.2 M lithium sulfate, 0.1 M phosphate-citrate pH 4.2, 20% PEG 1000. 25% Structure Screen 1 & 2 A11: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate, pH 4.6, 20% w/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 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: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→57.98 Å / Num. obs: 15396 / % possible obs: 99.83 % / Redundancy: 49.9 % / Biso Wilson estimate: 69.96 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1387 / Rpim(I) all: 0.02015 / Rrim(I) all: 0.1402 / Net I/σ(I): 15.29
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 50.6 % / Rmerge(I) obs: 0.6924 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1488 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.0976 / Rrim(I) all: 0.6993 / % possible all: 99.07

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→57.98 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
Details: Waters and rotamer outliers were fixed with COOT(0.8.9.2).
RfactorNum. reflection% reflection
Rfree0.2719 768 4.99 %
Rwork0.2253 --
obs0.2276 15385 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.95 Å2
Refinement stepCycle: LAST / Resolution: 2.8→57.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 27 4 3864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053896
X-RAY DIFFRACTIONf_angle_d0.6545312
X-RAY DIFFRACTIONf_dihedral_angle_d9.903615
X-RAY DIFFRACTIONf_chiral_restr0.038741
X-RAY DIFFRACTIONf_plane_restr0.004659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.33731620.28582816X-RAY DIFFRACTION99
3.02-3.320.32361340.24142903X-RAY DIFFRACTION100
3.32-3.80.30061630.24922860X-RAY DIFFRACTION100
3.8-4.790.22271560.17842936X-RAY DIFFRACTION100
4.79-57.980.26891530.23543102X-RAY DIFFRACTION100
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)
15.3711-0.04440.95362.6701-0.45995.0746-0.08970.5971-0.5373-0.09370.030.00310.42390.62450.09720.4690.0540.0590.5094-0.06510.4811-19.6102-38.1193-14.1478
23.9933-0.0131-1.55713.83253.51468.79490.0932-0.04830.17760.52330.4103-0.10931.335-0.7709-0.30950.7689-0.1824-0.17830.60680.02040.587623.2605-38.9947-22.4684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 309)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 308)

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