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- PDB-6g65: Crystal structure of a parallel six-helix coiled coil CC-Type2-VV -

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Basic information

Entry
Database: PDB / ID: 6g65
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-VV
ComponentsCC-Type2-VV
KeywordsDE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / AB_INITIO / Resolution: 1.15 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-VV
B: CC-Type2-VV
C: CC-Type2-VV
D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV
G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV
J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)37,47212
Polymers37,47212
Non-polymers00
Water6,305350
1
A: CC-Type2-VV
B: CC-Type2-VV
C: CC-Type2-VV

A: CC-Type2-VV
B: CC-Type2-VV
C: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10260 Å2
ΔGint-85 kcal/mol
Surface area9380 Å2
MethodPISA
2
D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV

D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10210 Å2
ΔGint-96 kcal/mol
Surface area9320 Å2
MethodPISA
3
G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV

G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9810 Å2
ΔGint-92 kcal/mol
Surface area9460 Å2
MethodPISA
4
J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV

J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10400 Å2
ΔGint-81 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.561, 96.793, 56.400
Angle α, β, γ (deg.)90.000, 124.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-139-

HOH

21B-140-

HOH

31B-141-

HOH

41B-142-

HOH

51E-131-

HOH

61E-132-

HOH

71F-130-

HOH

81F-131-

HOH

91G-134-

HOH

101G-135-

HOH

111G-136-

HOH

121I-135-

HOH

131K-129-

HOH

141L-123-

HOH

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Components

#1: Protein/peptide
CC-Type2-VV


Mass: 3122.655 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.98 Å3/Da / Density % sol: 37.85 % / Mosaicity: 0.42 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5 mM Manganese(II) chloride tetrahydrate, 50 mM Sodium citrate and 1.25 M 1,6-Hexanediol

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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: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.15→14.28 Å / Num. obs: 99219 / % possible obs: 96.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 13.7 / Num. measured all: 622875 / Scaling rejects: 336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.15-1.176.30.32849900.9860.1440.35997.9
6.3-14.287.50.0685950.9920.030.07591.5

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Phasing

PhasingMethod: AB_INITIO

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.25data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
Arcimboldo4.0.0phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.15→13.88 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.1896 5029 5.1 %
Rwork0.1761 --
obs0.1767 98638 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.99 Å2 / Biso mean: 13.3263 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.15→13.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 350 3002
Biso mean---30.18 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072892
X-RAY DIFFRACTIONf_angle_d0.683934
X-RAY DIFFRACTIONf_chiral_restr0.042459
X-RAY DIFFRACTIONf_plane_restr0.004488
X-RAY DIFFRACTIONf_dihedral_angle_d19.2631088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16310.24651900.20193086327697
1.1631-1.17680.19262010.20363108330996
1.1768-1.19110.21781590.19153097325695
1.1911-1.20620.1971530.18783088324195
1.2062-1.2220.19541590.17543128328796
1.222-1.23880.19181520.17463116326895
1.2388-1.25640.17231240.17283115323995
1.2564-1.27520.14611730.16023040321394
1.2752-1.29510.18121720.153000317292
1.2951-1.31630.17651870.1542970315792
1.3163-1.3390.16681990.15963164336398
1.339-1.36330.16521720.16073152332498
1.3633-1.38950.18351570.16093222337998
1.3895-1.41790.1731560.16243145330197
1.4179-1.44870.16671800.15843160334097
1.4487-1.48230.15791680.14963149331797
1.4823-1.51930.14621620.14373082324495
1.5193-1.56040.15761600.14253085324594
1.5604-1.60620.14661740.1442943311791
1.6062-1.6580.16671600.14163197335798
1.658-1.71710.16551950.15523190338599
1.7171-1.78570.17052170.15533134335198
1.7857-1.86680.17511600.15793210337098
1.8668-1.9650.18441290.17913176330597
1.965-2.08770.18021580.19153132329095
2.0877-2.24830.17461460.16352973311991
2.2483-2.47340.17481520.1643188334098
2.4734-2.82870.23721630.19153275343899
2.8287-3.55390.19861890.1923218340798
3.5539-13.88130.26471620.23953066322892
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)
10.23620.0754-0.02250.0521-0.09370.1836-0.0133-0.02910.03130.4926-0.0211-0.2977-0.00390.0203-0.00180.10770.0109-0.03070.0722-0.00170.06425.77129.41877.1043
20.16460.02430.10050.15360.07920.31350.0265-0.0013-0.01860.0407-0.06030.38320.0381-0.0254-0.10350.0656-0.00210.020.0761-0.00830.09537.916446.787824.9912
30.19030.11530.07560.05540.02990.14240.0175-0.0092-0.01670.268-0.0560.18810.00890.006300.09330.00450.01920.06780.00140.0502-3.032729.12728.6432
40.1854-0.0983-0.10150.04790.04850.1586-0.0060.00630.0018-0.3374-0.05120.25750.0290.0009-00.0950.0029-0.01470.0672-0.00630.0711.189847.530816.1398
50.21-0.03930.03010.0498-0.0820.14250.02380.0047-0.0057-0.0715-0.0456-0.3470.00390.0245-0.00040.06770.0020.01080.065-0.00110.07069.069128.67-1.6755
60.1926-0.1089-0.01590.0613-0.02320.074-0.02490.0018-0.0366-0.3779-0.0254-0.1466-0.00340.0263-0.00010.10360.00430.02650.06940.00330.061320.154347.039314.758
70.23760.14290.01360.1171-0.04940.08640.0044-0.01140.00440.4701-0.0168-0.089-0.00860.0050.00010.10890.0044-0.01350.0671-0.00080.0471.978677.9588.9942
80.14030.02720.06860.06580.10650.18450.05170.0024-0.01050.2569-0.07920.2181-0.0043-0.0145-0.00010.0669-0.00330.02010.06760.00030.07199.8151-0.560529.4746
90.07530.10210.07740.0740.0950.21590.0137-0.0104-0.03030.3339-0.0290.3762-0.0206-0.0095-0.00040.08030.00510.03430.07070.00530.0765-6.692377.82776.3651
100.03040.0222-0.11240.0828-0.1740.25850.0218-0.00690.0060.2792-0.0266-0.57440.00490.0094-0.09490.05960.0023-0.03320.0729-0.0050.12319.151577.72922.7924
110.2557-0.1142-0.00880.15420.00670.01060.04620.0321-0.0023-0.578-0.09710.0547-0.00430.0058-0.00130.12150.0049-0.01150.070.00020.056615.2157-0.71914.1341
120.0928-0.0843-0.1370.07660.15990.30460.06690.0199-0.006-0.1148-0.08850.55990.0019-0.009-0.00210.04540.0006-0.02750.06860.0010.11018.2793-1.173620.4274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 30 )H1 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 30 )A1 - 30
3X-RAY DIFFRACTION3chain 'G' and (resid 1 through 30 )G1 - 30
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 30 )B1 - 30
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 30 )I1 - 30
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 30 )C1 - 30
7X-RAY DIFFRACTION7chain 'K' and (resid 1 through 30 )K1 - 30
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 30 )D1 - 30
9X-RAY DIFFRACTION9chain 'J' and (resid 1 through 30 )J1 - 30
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 30 )L1 - 30
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 30 )F1 - 30
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 30 )E1 - 30

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