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- PDB-6g6b: Crystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17Q -

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Basic information

Entry
Database: PDB / ID: 6g6b
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-LL-L17Q
ComponentsCC-Type2-LL-L17Q
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: 2.3 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Type2-LL-L17Q
B: CC-Type2-LL-L17Q
C: CC-Type2-LL-L17Q


Theoretical massNumber of molelcules
Total (without water)9,7503
Polymers9,7503
Non-polymers00
Water25214
1
A: CC-Type2-LL-L17Q
B: CC-Type2-LL-L17Q
C: CC-Type2-LL-L17Q

A: CC-Type2-LL-L17Q
B: CC-Type2-LL-L17Q
C: CC-Type2-LL-L17Q


Theoretical massNumber of molelcules
Total (without water)19,4996
Polymers19,4996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area8830 Å2
ΔGint-91 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.790, 104.790, 104.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

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Components

#1: Protein/peptide CC-Type2-LL-L17Q


Mass: 3249.842 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.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.92 Å3/Da / Density % sol: 74.99 % / Mosaicity: 0.25 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 50 mM SPG Buffer (Succinic acid, Sodium phosphate monobasic monohydrate and Glycine) and 12.5% w/v PEG 1500

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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: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.3→74.1 Å / Num. obs: 9275 / % possible obs: 100 % / Redundancy: 65.4 % / Biso Wilson estimate: 53.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.01 / Rrim(I) all: 0.083 / Net I/σ(I): 38 / Num. measured all: 607009 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.3-2.3856.11.3658970.8870.1821.378
8.91-74.150.80.03121610.0040.031

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.91 Å74.1 Å
Translation5.91 Å74.1 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→74.098 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.2486 453 4.9 %
Rwork0.2165 --
obs0.2182 9242 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.37 Å2 / Biso mean: 60.5363 Å2 / Biso min: 36.11 Å2
Refinement stepCycle: final / Resolution: 2.3→74.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 14 684
Biso mean---66.65 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01680
X-RAY DIFFRACTIONf_angle_d1.309907
X-RAY DIFFRACTIONf_chiral_restr0.04106
X-RAY DIFFRACTIONf_plane_restr0.005111
X-RAY DIFFRACTIONf_dihedral_angle_d20.466261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3004-2.63330.30041490.260828502999
2.6333-3.31770.31791420.282328793021
3.3177-74.13620.21811620.190430603222

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