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

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Basic information

Entry
Database: PDB / ID: 8qab
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil hexameric alpha-helical barrel with 4 heptad repeats, apCCHex
ComponentsapCCHex
KeywordsDE NOVO PROTEIN / COILED COIL / alpha-helical barrel / DE NOVO PROTEIN DESIGN / PEPTIDE ASSEMBLY
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.4 Å
AuthorsNaudin, E.N. / Albanese, 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 1.2Oct 23, 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: apCCHex
B: apCCHex
C: apCCHex
D: apCCHex
E: apCCHex
F: apCCHex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9507
Polymers20,4196
Non-polymers5311
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-131 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.078, 30.914, 51.953
Angle α, β, γ (deg.)90.000, 88.642, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein/peptide
apCCHex


Mass: 3403.192 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-P8R / 1-methoxy-2-[2-[2-[2-[2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethane


Mass: 530.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.4→34.88 Å / Num. obs: 29174 / % possible obs: 99.83 % / Redundancy: 6 % / Biso Wilson estimate: 20.99 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03595 / Rpim(I) all: 0.01597 / Rrim(I) all: 0.03944 / Net I/σ(I): 22.17
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.8515 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 2850 / CC1/2: 0.625 / CC star: 0.877 / Rpim(I) all: 0.421 / Rrim(I) all: 0.9542 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.4→34.88 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 21.0482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 1415 4.86 %
Rwork0.1739 27712 -
obs0.1746 29127 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.45 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 36 143 1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051330
X-RAY DIFFRACTIONf_angle_d1.11941788
X-RAY DIFFRACTIONf_chiral_restr0.048242
X-RAY DIFFRACTIONf_plane_restr0.0064201
X-RAY DIFFRACTIONf_dihedral_angle_d4.874211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.33491580.29272692X-RAY DIFFRACTION99.2
1.45-1.510.24271310.21982729X-RAY DIFFRACTION99.51
1.51-1.580.26131550.1952738X-RAY DIFFRACTION99.93
1.58-1.660.20681440.19462740X-RAY DIFFRACTION99.97
1.66-1.760.25251380.20272785X-RAY DIFFRACTION100
1.76-1.90.21481520.18392752X-RAY DIFFRACTION99.97
1.9-2.090.19381350.16732796X-RAY DIFFRACTION99.97
2.09-2.390.18251270.14862779X-RAY DIFFRACTION100
2.39-3.020.16161530.16772798X-RAY DIFFRACTION100
3.02-34.880.17451220.17142903X-RAY DIFFRACTION99.8
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)
18.017026022350.709884877081-0.2993289378122.653290247470.1573340375062.432333809780.0993978387628-0.543443319863-0.2880030963890.160260851391-0.08827215678490.05865070230750.0249040986926-0.147162369069-0.01904811439890.225610465821-0.005601239228810.004719421801330.1455626747170.015010611360.1496719553638.4107936550927.660664152421.8400820399
27.82473145774-1.81464858571-1.982742734812.53010738419-0.106289987912.42855541490.2568476710140.0837392159590.5104665321410.028737748584-0.166489095003-0.229296263403-0.203688145469-0.0517659434838-0.1089200462680.2099561837610.00295571339207-0.005609131239780.122246244004-0.02137860612130.1709157256512.651615573436.388885981218.4073437411
39.27134213899-2.006489214753.754436816153.04327229648-0.585321223372.868616569360.357854255301-0.294072298999-0.4441465142180.015353567736-0.11414078797-0.1071718984110.407997518571-0.0597739414262-0.2644048503310.334051635754-0.01835457474780.01285452089980.1510107824020.01340932170120.16883578105710.870512650620.818875703516.7332156008
43.99575320534-2.70872491131-0.9605666759294.361660251490.2112813628031.694431333960.4516940839770.5735545901910.073299367199-0.711907981127-0.355694212222-0.2950457270470.1216564666370.138529418738-0.07354644346890.2979907667560.03417870223240.05363704846510.2054312708250.01753105143330.16044296924111.881836400129.52488147683.81214918896
58.92691487597-1.67927331218-2.469968054992.74118492871-0.1619237228733.904378017190.303171206421-0.2395073997220.386812662007-0.142143458676-0.198221612658-0.145753226815-0.2126781510240.0612734854418-0.12444359450.213261416122-0.02426453053440.01825486592170.1135855867750.0130285406570.1441863776819.0008598866137.956044519210.166622732
64.67695630493-4.18669469132.980228959754.57310886008-2.007539592332.142918544190.4886292285730.481413668523-0.404511451697-0.368179015915-0.3000321978130.1584015983410.4755230928060.100889309406-0.1609040296370.3205662241970.009201847999760.004387237197210.183028254263-0.02973772645730.1457005789146.7090287649923.05299023386.76771586191
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 1 through 30)AA1 - 301 - 30
22(chain 'B' and resid 0 through 31)BB - D0 - 31
33(chain 'C' and resid 1 through 30)CE1 - 301 - 30
44(chain 'D' and resid 1 through 31)DF - G1 - 311
55(chain 'E' and resid 1 through 30)EH1 - 301 - 30
66(chain 'F' and resid 1 through 29)FI1 - 291 - 29

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