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

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Basic information

Entry
Database: PDB / ID: 8qac
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil 8-helix bundle with 4 heptad repeats, antiparallel 8-helix bundle-GLIA
Componentsantiparallel 8-helix bundle-GLIA
KeywordsDE NOVO PROTEIN / COILED COIL / 8-HELIX BUNDLE / DE NOVO PROTEIN DESIGN / PEPTIDE ASSEMBLY
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å
AuthorsAlbanese, K.I. / Dawson, W.M. / 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: antiparallel 8-helix bundle-GLIA
C: antiparallel 8-helix bundle-GLIA
D: antiparallel 8-helix bundle-GLIA
E: antiparallel 8-helix bundle-GLIA
F: antiparallel 8-helix bundle-GLIA
G: antiparallel 8-helix bundle-GLIA
H: antiparallel 8-helix bundle-GLIA
I: antiparallel 8-helix bundle-GLIA
J: antiparallel 8-helix bundle-GLIA
K: antiparallel 8-helix bundle-GLIA
L: antiparallel 8-helix bundle-GLIA
N: antiparallel 8-helix bundle-GLIA
O: antiparallel 8-helix bundle-GLIA
P: antiparallel 8-helix bundle-GLIA
R: antiparallel 8-helix bundle-GLIA
M: antiparallel 8-helix bundle-GLIA


Theoretical massNumber of molelcules
Total (without water)51,77316
Polymers51,77316
Non-polymers00
Water36020
1
B: antiparallel 8-helix bundle-GLIA
E: antiparallel 8-helix bundle-GLIA
F: antiparallel 8-helix bundle-GLIA
G: antiparallel 8-helix bundle-GLIA
H: antiparallel 8-helix bundle-GLIA
I: antiparallel 8-helix bundle-GLIA
N: antiparallel 8-helix bundle-GLIA
R: antiparallel 8-helix bundle-GLIA


Theoretical massNumber of molelcules
Total (without water)25,8878
Polymers25,8878
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-152 kcal/mol
Surface area9320 Å2
MethodPISA
2
C: antiparallel 8-helix bundle-GLIA
D: antiparallel 8-helix bundle-GLIA
O: antiparallel 8-helix bundle-GLIA
M: antiparallel 8-helix bundle-GLIA

J: antiparallel 8-helix bundle-GLIA
K: antiparallel 8-helix bundle-GLIA
L: antiparallel 8-helix bundle-GLIA
P: antiparallel 8-helix bundle-GLIA


Theoretical massNumber of molelcules
Total (without water)25,8878
Polymers25,8878
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area11200 Å2
ΔGint-146 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.271, 45.873, 72.880
Angle α, β, γ (deg.)90.000, 103.943, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein/peptide
antiparallel 8-helix bundle-GLIA


Mass: 3235.819 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each alcohol, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→35.68 Å / Num. obs: 20647 / % possible obs: 99.51 % / Redundancy: 7 % / Biso Wilson estimate: 44.65 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.08693 / Rpim(I) all: 0.03623 / Rrim(I) all: 0.09436 / Net I/σ(I): 14.52
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.6312 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 2038 / CC1/2: 0.903 / CC star: 0.974 / Rpim(I) all: 0.2564 / Rrim(I) all: 0.6822 / % possible all: 99.46

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.3→35.68 Å / SU ML: 0.2706 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2828 1033 5.02 %
Rwork0.2267 19525 -
obs0.2292 20558 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 0 20 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00142964
X-RAY DIFFRACTIONf_angle_d0.28313990
X-RAY DIFFRACTIONf_chiral_restr0.0288497
X-RAY DIFFRACTIONf_plane_restr0.0008488
X-RAY DIFFRACTIONf_dihedral_angle_d2.4487439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.28791620.24192752X-RAY DIFFRACTION99.59
2.42-2.570.2731360.22582761X-RAY DIFFRACTION99.76
2.57-2.770.28351470.23752773X-RAY DIFFRACTION99.62
2.77-3.050.27491860.21572745X-RAY DIFFRACTION99.39
3.05-3.490.29091450.22632769X-RAY DIFFRACTION99.66
3.49-4.40.23891180.20122838X-RAY DIFFRACTION99.93
4.4-35.680.31251390.24692887X-RAY DIFFRACTION99.05
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)
14.564868391853.07164202792-5.495531787524.98471701656-4.217205053987.7815305710.196888772440.0582009295653-0.3733872201680.853127649131-0.118502655636-0.175280863746-0.5888649019760.00677870686204-0.1994859648090.5741012109220.00531989694712-0.08269645396740.4712759831040.01063645190840.386867006543-51.9358134404-7.3982231647-43.4404511186
28.7427781021-3.76259052625-6.244324352925.752193791043.77505295476.05191244228-0.8541607372210.137761170468-1.627712269570.5028875360170.1616312120950.9954049946260.170558249259-0.07679079680310.5672264550450.4197634243930.0437936426602-0.05253706017720.438166801844-0.0349510751030.397060039894-41.5266950373-10.7224591547-27.0957260126
38.02273634664-1.07517365281-8.034840310051.703673752061.610348405088.955554603610.64747233956-0.6651958274070.1422819495610.0778449529286-0.225538916512-0.0993901643702-0.8006707703560.410401593629-0.4285952700340.668966750040.0720664533565-0.118735586960.379084606353-0.05843415679280.519970944168-34.3444531028-6.09833512374-26.5996694648
46.293576449763.48913735572-6.852943523423.6082475005-3.063736117757.781529686830.3787217356920.2928764911380.2795050187740.43244873888-0.0884612511910.326074976728-0.235880033995-0.124844800859-0.1328969539080.515152976520.0247174503092-0.1080933042680.3825070612010.03650304132650.307205036209-49.7222183087-12.5632693195-50.2628518395
54.0118115935-3.06239946502-2.769973331927.005923205734.149932924625.92105387139-0.118908291883-0.0046574580207-1.0126991109-0.504506465186-0.4211877357060.807851913239-0.322004534152-0.7611563686180.06800514821680.3941123727960.039464438738-0.02240004575230.5443881876750.003166914039530.312746656345-65.4729221299-11.5746082595-61.0380365087
64.38392930286-1.94137038477-3.647605338832.468719010930.02027724389318.2270542848-0.484608811930.043536816042-0.6700672539850.1397411816330.125844842717-0.06554174534630.359621451426-0.08700752649080.3652316507930.449560278892-0.051179618029-0.07931705002560.210161946580.03403904130360.329014340862-58.4500676544-16.2385810043-53.1482424889
75.10067124665-1.457311604760.6114262282823.755174201040.01353440572783.707880733930.361174219792-0.386487977672-0.0262029965838-0.0402349702613-0.222255553452-0.1876235896670.2712316368930.174775350912-0.1302235447460.390586752538-0.09942774323330.06564268256830.278084388711-0.01851415108730.295085330723-61.041084684-20.9646314561-61.7603749682
88.784480874691.17494588119-5.478157270922.38596144379-1.208125845256.581366789930.006733376396390.3249972945380.3668133494210.595317774661-0.154133133064-0.06569702248-0.567862989788-0.6508120990820.001568877997480.6751538254340.0836272861298-0.1266514423490.38702131952-0.06064645471730.436678611402-58.4220322306-2.80000286874-51.2821147567
99.944240536070.767807848898-5.940836930041.86385417128-0.4230429639357.948149792670.17122176466-0.1653571355671.0815019446-0.600275375550.2500507830140.32343785149-0.3687595196180.420602166496-0.05896215272880.594304118446-0.0543955941241-0.196637712430.4538076133110.07154533843430.370802353262-20.0522740128-25.8737264888-52.531080684
107.85856633847-0.759865587419-2.435697233544.270922951531.325701900781.03058349045-0.5292075915550.3676052934210.553111132024-0.4747886568730.623853382068-0.558340603904-0.01675658824490.2096748937450.05373327194130.6824555932440.00424016142501-0.2450171251160.511359216583-0.1220799095030.595555545896-27.6187541637-35.6804719469-55.9271454339
111.73127529467-1.10948576985-2.90543242622.26328522842.198666974324.92398048340.593138717436-0.2296419716230.837950299671-0.5915725442990.159910326807-0.487587983443-0.1377309540830.71718874401-0.5907982798250.776680906810.0996416240571-0.1665491465530.642106881266-0.0258355215340.53425805313-24.7219958282-29.9776286389-61.5651453559
126.432859173291.92274032752-2.721789909912.76716053031-0.2526223221922.61360425019-0.2209278605550.0587908403174-0.06920115864950.18381565352-0.1145393773020.216091302184-0.345201339744-0.3452602997920.4171190312670.4727117550370.00872375201982-0.05918754571610.283726960782-0.009758283167840.46978941419-49.65412384531.91410480726-48.3881004024
138.31369769718-7.30336734509-1.762239385767.302116963452.184643251193.899236404920.701043862581-0.00667692123726-0.0648968897948-0.179101836248-0.5991691120750.5009846160320.0644348729813-0.533713236926-0.11725301560.436978733655-0.04493562364940.03905284031520.335619162527-0.08362718225560.625669189531-36.6136748928-20.0509158368-27.774734395
143.907751066820.9417591299742.159048257611.63460420054-1.09263825183.03187594297-0.1735551122330.5021788700840.5801337813750.2469685841650.00529552750023-0.0216882369530.318305600101-0.0724487654277-0.04039287076720.7677981647440.0291751114254-0.1500684453390.5447280521540.2022507390230.683048889296-26.8170462036-21.1744754896-58.395463444
158.01264078232-3.05038242294-7.972793096662.140241476422.508050143158.18587097832-0.0554319195817-0.1580331448830.05602479372790.256128090954-0.130685232315-0.0190382125266-0.540207866901-0.1818744164490.05673823084210.5086455028180.00967097270427-0.04356722970030.4037447627470.03503220958880.338788009477-58.6834869312-6.37641252414-61.6147873162
162.00144711655-0.709396990982-6.110594491821.7433872351-0.134473400666.1168148704-0.2381406798940.209970493175-1.85322226828-0.104747368878-0.06059172314290.2125451907880.150271035699-0.007071684605350.06282153953270.651515647295-0.0968527026765-0.2399014955540.3364807640720.08364925931910.548039320196-34.7371514959-15.8531217686-18.8872931781
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 1 through 30)BA1 - 301 - 30
22(chain 'C' and resid 1 through 30)CB1 - 301 - 30
33(chain 'D' and resid 2 through 29)DC2 - 291 - 28
44(chain 'E' and resid 1 through 30)ED1 - 301 - 30
55(chain 'F' and resid 1 through 29)FE1 - 291 - 29
66(chain 'G' and resid 1 through 29)GF1 - 291 - 29
77(chain 'H' and resid 3 through 29)HG3 - 291 - 27
88(chain 'I' and resid 2 through 29)IH2 - 291 - 28
99(chain 'J' and resid 2 through 28)JI2 - 281 - 27
1010(chain 'K' and resid 2 through 29)KJ2 - 291 - 28
1111(chain 'L' and resid 1 through 29)LK1 - 291 - 29
1212(chain 'N' and resid 2 through 29)NL2 - 291 - 28
1313(chain 'O' and resid 2 through 29)OM2 - 291 - 28
1414(chain 'P' and resid 2 through 29)PN2 - 291 - 28
1515(chain 'R' and resid 2 through 30)RO2 - 301 - 29
1616(chain 'M' and resid 2 through 29)MP2 - 291 - 28

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