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- PDB-6g6d: Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-Sg -

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Basic information

Entry
Database: PDB / ID: 6g6d
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-LL-Sg
ComponentsCC-Type2-LL-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: 2.05 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-LL-Sg
B: CC-Type2-LL-Sg
C: CC-Type2-LL-Sg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9894
Polymers9,8973
Non-polymers921
Water30617
1
A: CC-Type2-LL-Sg
B: CC-Type2-LL-Sg
C: CC-Type2-LL-Sg
hetero molecules

A: CC-Type2-LL-Sg
B: CC-Type2-LL-Sg
C: CC-Type2-LL-Sg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9778
Polymers19,7936
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area10260 Å2
ΔGint-92 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.160, 104.160, 104.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

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


Mass: 3298.871 Da / Num. of mol.: 3 / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 17 / 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

CrystalMosaicity: 0.26 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Potassium formate and 10 % w/v PEG 3350

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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: 2.05→73.65 Å / Num. obs: 12704 / % possible obs: 100 % / Redundancy: 70 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.019 / Rrim(I) all: 0.154 / Net I/σ(I): 25.2 / Num. measured all: 889357 / Scaling rejects: 1550
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.1169.88.7999570.4321.0568.863100
8.94-73.6553.90.092080.9970.0120.09199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.16 Å60.14 Å
Translation4.16 Å60.14 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→73.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.141 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 601 4.7 %RANDOM
Rwork0.1996 ---
obs0.2007 12054 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 62.853 Å2 / Biso min: 37.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.05→73.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 6 17 716
Biso mean--116.48 66.61 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.02736
X-RAY DIFFRACTIONr_bond_other_d0.0060.02754
X-RAY DIFFRACTIONr_angle_refined_deg3.3092.04996
X-RAY DIFFRACTIONr_angle_other_deg1.3722.9981772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30326.66724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68115161
X-RAY DIFFRACTIONr_chiral_restr0.1920.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02117
LS refinement shellResolution: 2.051→2.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 39 -
Rwork0.375 862 -
all-901 -
obs--100 %
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)
13.50371.05361.97790.53051.3483.7874-0.06380.011-0.036-0.0229-0.05930.0395-0.0935-0.24950.12310.14470.050.11820.13050.02850.112114.85612.15820.2359
22.62070.18993.42660.2106-0.34126.4907-0.2273-0.0764-0.2128-0.0872-0.0865-0.17080.0029-0.02450.31370.12210.00030.16420.13-0.0010.253620.04456.997-2.203
36.69541.03481.99990.55311.10082.19980.37210.0886-0.171-0.2914-0.1106-0.1436-0.5938-0.274-0.26160.32920.13860.09510.13210.01010.065913.259519.6233-1.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0 - 30
2X-RAY DIFFRACTION2A0 - 30
3X-RAY DIFFRACTION3C1 - 30

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