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

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Basic information

Entry
Database: PDB / ID: 8qkd
TitleX-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 5 inner helices, sc-CC-5-24
Componentssc-CC-5-24
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: 1.9 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
DepositionSep 15, 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-5-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6783
Polymers30,4661
Non-polymers2122
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint7 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)91.981, 41.359, 62.556
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein sc-CC-5-24


Mass: 30466.117 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.89 Å3/Da / Density % sol: 34.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: JCSG+ D2: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES, pH 7.5, 30 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.9→60.54 Å / Num. obs: 18195 / % possible obs: 99.83 % / Redundancy: 10.1 % / Biso Wilson estimate: 35.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05919 / Rpim(I) all: 0.01955 / Rrim(I) all: 0.06239 / Net I/σ(I): 20.16
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.4768 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 1817 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.1717 / Rrim(I) all: 0.5075 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→60.54 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22 / Stereochemistry target values: ML
Details: Waters and rotamer outliers were fixed with COOT(0.8.9.2) before deposition.
RfactorNum. reflection% reflection
Rfree0.2154 895 4.92 %
Rwork0.1873 --
obs0.1887 18174 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→60.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 14 66 2004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021967
X-RAY DIFFRACTIONf_angle_d0.4432682
X-RAY DIFFRACTIONf_dihedral_angle_d3.444293
X-RAY DIFFRACTIONf_chiral_restr0.033360
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.25941710.21552818X-RAY DIFFRACTION99
2.02-2.170.23631440.18312865X-RAY DIFFRACTION100
2.17-2.390.22021540.17792837X-RAY DIFFRACTION100
2.39-2.740.20711320.18142904X-RAY DIFFRACTION100
2.74-3.450.23321450.19842897X-RAY DIFFRACTION100
3.45-60.540.19881490.18352958X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.6315 Å / Origin y: 1.2173 Å / Origin z: 15.2797 Å
111213212223313233
T0.238 Å20.0035 Å20.0215 Å2-0.2548 Å20.0092 Å2--0.2564 Å2
L3.3038 °2-0.1388 °21.3793 °2-2.0932 °2-0.3361 °2--3.0148 °2
S-0.0006 Å °-0.1532 Å °0.0623 Å °0.0135 Å °-0.0086 Å °0.1235 Å °0.0654 Å °-0.056 Å °0.0098 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 280)

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