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

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Basic information

Entry
Database: PDB / ID: 8qai
TitleX-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 7 inner helices, sc-CC-7-LI
Componentssc-CC-7-LI
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: 2.5 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-7-LI
B: sc-CC-7-LI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9673
Polymers78,8612
Non-polymers1061
Water41423
1
A: sc-CC-7-LI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,4311
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sc-CC-7-LI


Theoretical massNumber of molelcules
Total (without water)39,4311
Polymers39,4311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.207, 54.025, 74.930
Angle α, β, γ (deg.)99.40, 100.94, 105.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein sc-CC-7-LI


Mass: 39430.688 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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: JCSG-plus C2: 1.0 M Lithium chloride, 0.1 M citrate, pH 4.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.5→30.63 Å / Num. obs: 23776 / % possible obs: 98.44 % / Redundancy: 2.5 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.08575 / Rpim(I) all: 0.06252 / Rrim(I) all: 0.1068 / Net I/σ(I): 9.11
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.2149 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2330 / CC1/2: 0.923 / CC star: 0.98 / Rpim(I) all: 0.1616 / Rrim(I) all: 0.2704 / % possible all: 97.24

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.63 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1572 6.62 %
Rwork0.199 --
obs0.2015 23743 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4827 0 7 23 4857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024844
X-RAY DIFFRACTIONf_angle_d0.2636608
X-RAY DIFFRACTIONf_dihedral_angle_d15.4921554
X-RAY DIFFRACTIONf_chiral_restr0.029918
X-RAY DIFFRACTIONf_plane_restr0.001818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.29751430.21782010X-RAY DIFFRACTION97
2.58-2.670.24181400.20411984X-RAY DIFFRACTION98
2.67-2.780.25661440.18762017X-RAY DIFFRACTION98
2.78-2.910.27651420.19621997X-RAY DIFFRACTION98
2.91-3.060.26431420.20142012X-RAY DIFFRACTION99
3.06-3.250.25091450.19252042X-RAY DIFFRACTION99
3.25-3.50.26051420.22071991X-RAY DIFFRACTION99
3.5-3.850.2271450.18542050X-RAY DIFFRACTION99
3.85-4.410.17481450.16152032X-RAY DIFFRACTION99
4.41-5.550.24871430.21462020X-RAY DIFFRACTION99
5.55-30.630.23241410.22232016X-RAY DIFFRACTION98
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)
11.8252-0.13320.73691.8162-0.07153.8795-0.00880.12670.06270.11580.0122-0.2133-0.14570.2828-0.00930.2761-0.0288-0.04430.3573-0.05540.25535.265515.214732.9429
21.7320.2005-0.08421.458-0.09631.3334-0.00130.0198-0.0134-0.01830.03170.0210.03920.03-0.02230.2405-0.0266-0.02470.2795-0.00630.20883.3310.3391-3.0493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid -1 through 366)
2X-RAY DIFFRACTION2(chain 'A' and resid -1 through 368)

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