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- PDB-7bo9: A hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W1... -

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Basic information

Entry
Database: PDB / ID: 7bo9
TitleA hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W19(BrPhe).
ComponentsCC-Type2-(VaYd)4-Y3F-W19(BrPhe)
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly / tyrosine-tyrosine interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Biomacromolecules / Year: 2021
Title: How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues.
Authors: Rhys, G.G. / Dawson, W.M. / Beesley, J.L. / Martin, F.J.O. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionJan 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
B: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
C: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
D: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
E: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
F: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5087
Polymers20,4166
Non-polymers921
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-84 kcal/mol
Surface area9770 Å2
Unit cell
Length a, b, c (Å)44.630, 50.900, 69.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
CC-Type2-(VaYd)4-Y3F-W19(BrPhe)


Mass: 3402.687 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 0.1 M sodium sulphate, 0.05 M Bis-Tris propane and 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.56→50.9 Å / Num. obs: 23181 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.21 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.03 / Rrim(I) all: 0.105 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allCC star
6.98-50.9100.06531.23140.9970.0210.06997.9
1.56-1.611.81.9751.316720.6090.5972.06499.50.867

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSNov 11, 2017data reduction
XSCALENov 11, 2017data scaling
xia20.5.482-g030776d9-dials-1.8data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→41.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.87 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1161 5 %RANDOM
Rwork0.1874 ---
obs0.1901 21969 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.71 Å2 / Biso mean: 30.69 Å2 / Biso min: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---1.45 Å20 Å2
3---3.04 Å2
Refinement stepCycle: final / Resolution: 1.56→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 6 146 1563
Biso mean--58.42 40.91 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181429
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.6671947
X-RAY DIFFRACTIONr_angle_other_deg1.4931.6153309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8315171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46324.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51115252
X-RAY DIFFRACTIONr_chiral_restr0.0890.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
LS refinement shellResolution: 1.56→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 88 -
Rwork0.306 1583 -
all-1671 -
obs--99.58 %
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)
13.16260.13221.22340.42260.0120.6850.0385-0.0047-0.224-0.01070.0116-0.04390.01040.0076-0.05010.08140.0017-0.01020.09960.0020.043927.2279-4.371850.1412
23.9962-1.1953-0.20361.22590.35410.11580.13730.0930.078-0.3117-0.0874-0.1099-0.1017-0.0168-0.04980.12480.020.04240.11120.01320.045228.64016.651738.5788
35.17151.66690.4831.19790.43010.1623-0.0591-0.08480.04120.05170.02660.0530.0180.0090.03250.0776-0.00770.00050.10010.00120.053621.96412.236153.1859
43.8655-1.12351.51032.12580.23130.83990.02320.1406-0.1987-0.44260.0781-0.0087-0.1540.1016-0.10130.1538-0.00060.00690.1081-0.00840.014827.6943-0.87436.8308
53.2292-0.01092.07030.28040.17471.5649-0.05910.1572-0.1231-0.10750.00210.0478-0.06230.10020.0570.12830.00520.00160.0849-0.02680.113922.1912-7.033838.923
63.0312-0.1322-0.10010.6013-0.09930.03540.039-0.0520.0848-0.0685-0.01850.0147-0.02370.0032-0.02050.1029-0.00290.0170.0971-0.00480.041121.07118.544148.3326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E0 - 29
6X-RAY DIFFRACTION6F1 - 30

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