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- PDB-6g66: Crystal structure of a parallel seven-helix coiled coil CC-Type2-IV -

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Basic information

Entry
Database: PDB / ID: 6g66
TitleCrystal structure of a parallel seven-helix coiled coil CC-Type2-IV
ComponentsCC-Type2-IV
KeywordsDE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
Authors: Rhys, G.G. / Wood, C.W. / Lang, E.J.M. / Mulholland, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: 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-IV
B: CC-Type2-IV
C: CC-Type2-IV
D: CC-Type2-IV
E: CC-Type2-IV
F: CC-Type2-IV
G: CC-Type2-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4369
Polymers22,2517
Non-polymers1842
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-107 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.240, 48.350, 130.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-138-

HOH

21E-122-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 30
211chain BB0 - 30
311chain CC0 - 31
411chain DD0 - 31
511chain EE0 - 30
611chain FF0 - 30
711chain GG0 - 30

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Components

#1: Protein/peptide
CC-Type2-IV


Mass: 3178.763 Da / Num. of mol.: 7 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.46 % / Mosaicity: 1.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 50 mM HEPES and 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→48.34 Å / Num. obs: 35569 / % possible obs: 99.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 20.04 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.073 / Rrim(I) all: 0.238 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.5810.71.4217210.7750.4471.49298.1
8.49-48.3410.20.2052820.9770.0670.21699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.55 Å45.31 Å
Translation5.57 Å45.31 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.318 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2414 1661 5.14 %
Rwork0.2036 --
obs0.2053 32335 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.19 Å2 / Biso mean: 28.3835 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: final / Resolution: 1.6→45.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 12 203 1785
Biso mean--63.34 42.63 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071671
X-RAY DIFFRACTIONf_angle_d0.9172255
X-RAY DIFFRACTIONf_chiral_restr0.04263
X-RAY DIFFRACTIONf_plane_restr0.005274
X-RAY DIFFRACTIONf_dihedral_angle_d15.147641
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A856X-RAY DIFFRACTION6.593TORSIONAL
12B856X-RAY DIFFRACTION6.593TORSIONAL
13C856X-RAY DIFFRACTION6.593TORSIONAL
14D856X-RAY DIFFRACTION6.593TORSIONAL
15E856X-RAY DIFFRACTION6.593TORSIONAL
16F856X-RAY DIFFRACTION6.593TORSIONAL
17G856X-RAY DIFFRACTION6.593TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64710.26621450.21852450259598
1.6471-1.70020.27891320.22392494262698
1.7002-1.7610.21771500.21192499264998
1.761-1.83150.25111450.20792483262898
1.8315-1.91490.25361490.1892517266699
1.9149-2.01580.28451340.22362547268199
2.0158-2.14210.26891390.19652539267899
2.1421-2.30750.22751410.18122564270599
2.3075-2.53970.23461220.18262584270699
2.5397-2.90720.21121340.190825942728100
2.9072-3.66250.22721330.20126432776100
3.6625-45.33570.25361370.22422760289799
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)
11.1623-0.28330.19681.1-1.39812.6835-0.1163-0.08440.14660.26730.051-0.0598-1.28030.02420.19080.2229-0.0105-0.0440.1236-0.03830.25348.256832.899523.9661
21.11720.0356-0.7161.1219-0.72042.4047-0.0764-0.0141-0.16530.0623-0.0278-0.04751.0043-0.28750.14790.2064-0.0396-0.00280.11580.02420.22336.377412.713122.8919
30.8942-0.1539-0.02261.0025-0.25786.0513-0.0713-0.04050.08980.2353-0.0259-0.1735-0.76050.61980.10210.1863-0.0779-0.05980.17330.01960.218816.40130.445322.7899
40.9827-0.08170.5161.556-2.07253.42670.12250.0455-0.07950.0592-0.0669-0.1271-0.00971.1283-0.06210.14460.0052-0.04060.26250.02260.270119.574521.678123.2064
51.20730.13790.18611.6969-0.99557.06240.0535-0.114-0.17460.02720.0055-0.17540.86480.63350.01420.16530.0572-0.03610.13940.02120.241215.095514.084923.2319
60.90410.0757-0.79281.65750.09932.15250.1126-0.04320.06630.24910.06390.034-0.3285-0.3328-0.11030.16040.01240.0110.1788-0.03480.21080.61627.837924.1016
71.40140.2245-0.15171.18590.57412.25480.0787-0.0651-0.00420.125-0.01920.04030.2556-0.7902-0.03220.135-0.0261-0.01370.19850.01530.2093-0.117419.021422.4196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A1 - 30
2X-RAY DIFFRACTION2chain 'D' and (resid 1 through 30 )D1 - 30
3X-RAY DIFFRACTION3chain 'G' and (resid 1 through 30 )G1 - 30
4X-RAY DIFFRACTION4chain 'F' and (resid 1 through 30 )F1 - 30
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 30 )E1 - 30
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 30 )B1 - 30
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 30 )C1 - 30

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