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- PDB-6g6g: Crystal structure of a parallel six-helix coiled coil CC-Type2-FI -

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Basic information

Entry
Database: PDB / ID: 6g6g
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-FI
ComponentsCC-Type2-FI
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: 1.7 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-FI
B: CC-Type2-FI
C: CC-Type2-FI
D: CC-Type2-FI
E: CC-Type2-FI
F: CC-Type2-FI
G: CC-Type2-FI
H: CC-Type2-FI
I: CC-Type2-FI
J: CC-Type2-FI
K: CC-Type2-FI
L: CC-Type2-FI


Theoretical massNumber of molelcules
Total (without water)40,45112
Polymers40,45112
Non-polymers00
Water4,846269
1
A: CC-Type2-FI
B: CC-Type2-FI
C: CC-Type2-FI
D: CC-Type2-FI
E: CC-Type2-FI
F: CC-Type2-FI


Theoretical massNumber of molelcules
Total (without water)20,2266
Polymers20,2266
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-105 kcal/mol
Surface area9720 Å2
MethodPISA
2
G: CC-Type2-FI
H: CC-Type2-FI
I: CC-Type2-FI
J: CC-Type2-FI
K: CC-Type2-FI
L: CC-Type2-FI


Theoretical massNumber of molelcules
Total (without water)20,2266
Polymers20,2266
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-107 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.660, 85.000, 59.608
Angle α, β, γ (deg.)90.000, 92.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
CC-Type2-FI


Mass: 3370.935 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.: 269 / 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: 1.92 Å3/Da / Density % sol: 35.88 % / Mosaicity: 1.4 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 50 mM Tris and 10 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.7→59.55 Å / Num. obs: 33463 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.069 / Rrim(I) all: 0.159 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.734.51.02517540.6560.5291.15899.6
9-59.555.10.0752450.9960.0360.08399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.42 Å48.77 Å
Translation4.42 Å48.77 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.773 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2215 1670 5 %
Rwork0.1756 --
obs0.1778 33430 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 24.5741 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 1.7→48.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 0 269 3150
Biso mean---35.76 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062982
X-RAY DIFFRACTIONf_angle_d0.6473968
X-RAY DIFFRACTIONf_chiral_restr0.044391
X-RAY DIFFRACTIONf_plane_restr0.004501
X-RAY DIFFRACTIONf_dihedral_angle_d16.31755
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 (%)
1.7-1.750.31591420.263625992741100
1.75-1.80650.30461490.2582655280499
1.8065-1.87110.28111500.249125842734100
1.8711-1.9460.26991620.236226242786100
1.946-2.03460.31781330.208626812814100
2.0346-2.14180.23211260.175126232749100
2.1418-2.2760.22951420.166426382780100
2.276-2.45180.23521240.169126582782100
2.4518-2.69850.22211340.169226652799100
2.6985-3.08890.19561350.164226752810100
3.0889-3.89140.20441270.155126782805100
3.8914-48.79290.17191460.15242680282699

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