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- PDB-6g68: Crystal structure of a parallel six-helix coiled coil CC-Type2-IL-Sg -

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Basic information

Entry
Database: PDB / ID: 6g68
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-IL-Sg
ComponentsCC-Type2-IL-Sg
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: 1.95 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
Revision 1.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-IL-Sg
B: CC-Type2-IL-Sg
C: CC-Type2-IL-Sg
D: CC-Type2-IL-Sg
E: CC-Type2-IL-Sg
F: CC-Type2-IL-Sg
G: CC-Type2-IL-Sg
H: CC-Type2-IL-Sg
I: CC-Type2-IL-Sg
J: CC-Type2-IL-Sg
K: CC-Type2-IL-Sg
L: CC-Type2-IL-Sg
M: CC-Type2-IL-Sg
N: CC-Type2-IL-Sg
O: CC-Type2-IL-Sg
P: CC-Type2-IL-Sg
Q: CC-Type2-IL-Sg
R: CC-Type2-IL-Sg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57220
Polymers59,38018
Non-polymers1922
Water4,161231
1
A: CC-Type2-IL-Sg
B: CC-Type2-IL-Sg
C: CC-Type2-IL-Sg
D: CC-Type2-IL-Sg
E: CC-Type2-IL-Sg
F: CC-Type2-IL-Sg


Theoretical massNumber of molelcules
Total (without water)19,7936
Polymers19,7936
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-107 kcal/mol
Surface area9010 Å2
MethodPISA
2
G: CC-Type2-IL-Sg
H: CC-Type2-IL-Sg
I: CC-Type2-IL-Sg
J: CC-Type2-IL-Sg
K: CC-Type2-IL-Sg
L: CC-Type2-IL-Sg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9858
Polymers19,7936
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-123 kcal/mol
Surface area9010 Å2
MethodPISA
3
M: CC-Type2-IL-Sg
N: CC-Type2-IL-Sg
O: CC-Type2-IL-Sg
P: CC-Type2-IL-Sg
Q: CC-Type2-IL-Sg
R: CC-Type2-IL-Sg


Theoretical massNumber of molelcules
Total (without water)19,7936
Polymers19,7936
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-99 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.361, 90.030, 112.470
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
11A-120-

HOH

21A-122-

HOH

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Components

#1: Protein/peptide
CC-Type2-IL-Sg


Mass: 3298.871 Da / Num. of mol.: 18 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.56 % / Mosaicity: 0.38 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Ammonium Sulfate and 15% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.95→90.03 Å / Num. obs: 43994 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.046 / Rrim(I) all: 0.16 / Net I/σ(I): 11.7 / Num. measured all: 530587 / Scaling rejects: 367
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-212.12.28430010.3280.6792.384100
8.94-90.03120.0425460.9990.0120.04499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.36 Å70.29 Å
Translation4.36 Å70.29 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→70.285 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.78
RfactorNum. reflection% reflection
Rfree0.2105 2119 4.82 %
Rwork0.1793 --
obs0.1809 43920 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.06 Å2 / Biso mean: 40.8303 Å2 / Biso min: 12.49 Å2
Refinement stepCycle: final / Resolution: 1.95→70.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 10 231 4385
Biso mean--92.16 47.13 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084409
X-RAY DIFFRACTIONf_angle_d0.8395927
X-RAY DIFFRACTIONf_chiral_restr0.044699
X-RAY DIFFRACTIONf_plane_restr0.004706
X-RAY DIFFRACTIONf_dihedral_angle_d20.622863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.99540.32471300.278527122842
1.9954-2.04530.28391400.250927582898
2.0453-2.10060.27391510.240627412892
2.1006-2.16240.24221380.204627542892
2.1624-2.23220.22331400.181127432883
2.2322-2.3120.19191270.179627612888
2.312-2.40460.22581490.171627542903
2.4046-2.5140.18631560.163727522908
2.514-2.64660.20951380.171527852923
2.6466-2.81240.23121320.184327982930
2.8124-3.02950.22161430.174927742917
3.0295-3.33440.20591320.175528122944
3.3344-3.81690.21511350.176128202955
3.8169-4.80870.17051450.149428603005
4.8087-70.33080.20551630.186629773140
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)
12.9068-1.40890.42928.4286-2.93782.9894-0.14-0.07350.25830.131-0.0055-1.0196-0.19280.21890.25550.1721-0.0213-0.03230.2580.01820.254349.096527.899822.3202
22.33071.3858-1.1124.4645-5.39455.0103-0.25280.20150.0525-0.49270.3631-0.30510.3493-0.0807-0.00620.1573-0.0328-0.03490.21840.01470.207745.587225.279414.9088
35.29854.0425-3.12946.8971-6.58916.9084-0.10250.3119-0.2245-1.35720.580.6530.8283-0.5138-0.44010.285-0.0909-0.14350.31980.10130.345137.78724.665412.2265
44.03460.7448-0.58312.92190.20140.20570.0391-0.0435-0.4752-0.19270.51850.76960.0894-0.4856-0.46430.2139-0.0574-0.10840.41820.20380.533630.345527.910814.1884
52.58190.96170.78848.6234.40233.64190.02030.0053-0.08360.17240.2254-0.4230.15060.3938-0.44190.1758-0.005-0.02690.23610.04470.178419.850935.35913.0007
61.32991.30340.34752.85622.98034.0607-0.0845-0.00980.10250.0976-0.12850.55470.2676-0.35150.30420.1532-0.05820.00470.2689-0.00620.2570.652833.64079.9909
70.981-0.1025-0.08644.43515.28295.5648-0.1426-0.2007-0.07160.8810.01730.57860.8089-0.20160.16580.2509-0.09480.03070.28280.010.20645.08431.675416.9447
81.2148-0.12-0.31092.28793.47786.40980.0134-0.0238-0.07130.7922-0.08620.04020.6154-0.0369-0.01050.2215-0.0483-0.0150.23130.02420.18913.755731.7117.2692
91.79821.09092.25943.51494.46377.4284-0.09180.02840.0883-0.3153-0.0910.2723-0.3957-0.17840.18720.1709-0.0093-0.00080.19990.02980.169310.967640.4227.1562
104.7623-2.482.16783.6202-4.78466.1437-0.2915-0.09540.39210.90230.1915-0.3046-0.696-0.0890.06770.21280.0194-0.03440.21330.00240.229544.937728.341629.6928
111.8547-2.02241.72435.3888-3.12424.3944-0.0951-0.1417-0.08860.25640.69011.0425-0.2855-0.6165-0.65530.16380.02690.01310.34860.12320.359735.036830.611222.0103
124.0173.27232.49516.93853.44593.2625-0.19010.3050.0927-0.57490.1731-0.2861-0.41250.3215-0.1640.1953-0.03760.02050.23810.06170.192420.50640.27956.0901
138.7557-4.8438-0.89519.1256-1.75084.7284-0.0697-0.3692-0.67730.6215-0.3698-0.19760.14020.56240.20820.4134-0.1176-0.0170.29950.12220.23680.292726.165647.4511
148.6681-0.3906-3.9332.93231.60136.093-0.0861-0.1048-0.26650.1882-0.2214-0.0232-0.19210.6740.31420.4089-0.09340.04480.37590.09090.223310.444634.169733.3206
157.4738-2.6785-2.71158.81770.95893.67110.39120.6787-0.3311-0.4361-0.6749-0.2138-0.18470.06570.35370.3281-0.00740.03360.25660.05050.23193.182830.24833.1265
166.7849-1.6622-1.01026.4001-0.80524.54520.0470.054-0.7892-0.0924-0.3635-0.12350.46260.32590.21990.3882-0.03490.01620.16530.0750.2514-0.577325.985439.518
178.8447-4.0354-4.36048.66011.66416.89890.8478-0.62030.77450.3293-0.7204-0.9078-0.80090.8188-0.06160.5243-0.2707-0.0220.41720.07510.31137.372335.359345.4791
185.9755-2.5979-1.07184.3577-1.08644.2294-0.0028-0.8386-0.05640.6774-0.3197-0.318-0.47150.89540.20250.4773-0.2482-0.09540.48130.12020.27553.772630.900853.2488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'O' and (resid 1 through 30 )O1 - 30
2X-RAY DIFFRACTION2chain 'P' and (resid 1 through 30 )P1 - 30
3X-RAY DIFFRACTION3chain 'Q' and (resid 1 through 30 )Q1 - 30
4X-RAY DIFFRACTION4chain 'R' and (resid 1 through 30 )R1 - 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
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 30 )D1 - 30
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 30 )A1 - 30
10X-RAY DIFFRACTION10chain 'N' and (resid 1 through 29 )N1 - 29
11X-RAY DIFFRACTION11chain 'M' and (resid 1 through 30 )M1 - 30
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 30 )F1 - 30
13X-RAY DIFFRACTION13chain 'K' and (resid 1 through 30 )K1 - 30
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 30 )H1 - 30
15X-RAY DIFFRACTION15chain 'I' and (resid 1 through 30 )I1 - 30
16X-RAY DIFFRACTION16chain 'J' and (resid 1 through 30 )J1 - 30
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 29 )G1 - 29
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 30 )L1 - 30

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