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- PDB-6g6a: Crystal structure of a parallel six-helix coiled coil CC-Type2-LL -

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Basic information

Entry
Database: PDB / ID: 6g6a
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-LL
ComponentsCC-Type2-LL
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: 2.701 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 1.1May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: CC-Type2-LL
B: CC-Type2-LL
C: CC-Type2-LL


Theoretical massNumber of molelcules
Total (without water)9,7053
Polymers9,7053
Non-polymers00
Water1629
1
A: CC-Type2-LL
B: CC-Type2-LL
C: CC-Type2-LL

A: CC-Type2-LL
B: CC-Type2-LL
C: CC-Type2-LL


Theoretical massNumber of molelcules
Total (without water)19,4096
Polymers19,4096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area8770 Å2
ΔGint-90 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.529, 103.529, 103.529
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


Mass: 3234.871 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.76 Å3/Da / Density % sol: 74.18 % / Mosaicity: 0.47 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 mM Sodium/Potassium phosphate, 50 mM Bis-Tris propane and 10 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→73.21 Å / Num. obs: 5654 / % possible obs: 100 % / Redundancy: 64.6 % / Biso Wilson estimate: 62.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.026 / Rrim(I) all: 0.211 / Net I/σ(I): 21.1 / Num. measured all: 365480 / Scaling rejects: 248
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.7-2.8367.41.8497300.640.2251.863
8.96-73.2147.70.05220510.0070.052

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.63 Å73.21 Å
Translation5.63 Å73.21 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: 2.701→73.206 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.267 279 4.97 %
Rwork0.2185 --
obs0.221 5616 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 64.4535 Å2 / Biso min: 34.07 Å2
Refinement stepCycle: final / Resolution: 2.701→73.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms671 0 0 9 680
Biso mean---62.84 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012674
X-RAY DIFFRACTIONf_angle_d1.598898
X-RAY DIFFRACTIONf_chiral_restr0.054108
X-RAY DIFFRACTIONf_plane_restr0.007107
X-RAY DIFFRACTIONf_dihedral_angle_d17.945422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7012-3.40320.3411340.259525902724
3.4032-73.23290.24531450.204927472892

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