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

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Basic information

Entry
Database: PDB / ID: 8qae
TitleX-ray crystal structure of a de novo designed single-chain antiparallel 6-helix alpha-helical barrel, sc-apCC-6-SLLA
Componentssc-apCC-6-SLLA
KeywordsDE NOVO PROTEIN / coiled coil / alpha-helical barrel / de novo protein design
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: sc-apCC-6-SLLA
C: sc-apCC-6-SLLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2244
Polymers52,2182
Non-polymers1,0052
Water2,684149
1
A: sc-apCC-6-SLLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8762
Polymers26,1091
Non-polymers7671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9920 Å2
MethodPISA
2
C: sc-apCC-6-SLLA
hetero molecules

C: sc-apCC-6-SLLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6954
Polymers52,2182
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4330 Å2
ΔGint-44 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.823, 42.176, 71.522
Angle α, β, γ (deg.)90.000, 123.509, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21C-409-

HOH

31C-428-

HOH

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Components

#1: Protein sc-apCC-6-SLLA


Mass: 26109.238 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-P5R / 2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol


Mass: 766.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H70O18
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M CaCl2, 0.1 M MES pH 6.0, 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 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→21.4 Å / Num. obs: 25168 / % possible obs: 99.84 % / Redundancy: 6.7 % / Biso Wilson estimate: 35.49 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.08096 / Rpim(I) all: 0.03443 / Rrim(I) all: 0.08813 / Net I/σ(I): 14.57
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4644 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 2501 / CC1/2: 0.903 / CC star: 0.974 / Rpim(I) all: 0.2069 / Rrim(I) all: 0.5099 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.4 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.6092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 1347 5.36 %
Rwork0.2057 23806 -
obs0.2069 25153 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 47 149 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252192
X-RAY DIFFRACTIONf_angle_d0.49932967
X-RAY DIFFRACTIONf_chiral_restr0.0201379
X-RAY DIFFRACTIONf_plane_restr0.0023351
X-RAY DIFFRACTIONf_dihedral_angle_d9.5174368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.26841230.28112377X-RAY DIFFRACTION99.96
1.97-2.050.28611300.23672368X-RAY DIFFRACTION100
2.05-2.140.27981420.21312337X-RAY DIFFRACTION100
2.14-2.250.21741460.19182368X-RAY DIFFRACTION99.92
2.25-2.390.21191340.18912347X-RAY DIFFRACTION100
2.39-2.580.20471310.1962388X-RAY DIFFRACTION100
2.58-2.840.26511600.21352343X-RAY DIFFRACTION100
2.84-3.250.22581410.21142390X-RAY DIFFRACTION100
3.25-4.080.18961020.19462426X-RAY DIFFRACTION100
4.08-21.40.23471380.20742462X-RAY DIFFRACTION99.5
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)
14.041371776110.890322239110.7167082277551.653319042720.03786998797672.052592173780.0246075864307-0.1170521774320.07648409282930.000234857381913-0.0799566123568-0.100617183134-0.1112272847910.06305914406650.03755515303480.165334648010.008578011750670.06905729686560.2530537880410.004979615588730.22383571424417.21540036730.4162314716383.7129676169
23.50835287748-0.407588743043-0.0844451307791.215001884250.1601245157361.978487108340.3600241276810.3824606915550.0833690943077-0.1540061572-0.2568881124520.0609461836508-0.166002032536-0.130377606953-0.1489506605370.3727568037020.01511547779540.05042634111920.3478046253790.01111081540020.16239225399640.2860586194-11.647129245924.4571490469
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid -3 through 212)AA-3 - 2121 - 212
22(chain 'C' and resid 106 through 211)CB106 - 2111 - 98

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