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- PDB-6g67: Crystal structure of a parallel eight-helix coiled coil CC-Type2-II -

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Basic information

Entry
Database: PDB / ID: 6g67
TitleCrystal structure of a parallel eight-helix coiled coil CC-Type2-II
ComponentsCC-Type2-II
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: 1.77 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-II
B: CC-Type2-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5623
Polymers6,4702
Non-polymers921
Water1,24369
1
A: CC-Type2-II
B: CC-Type2-II
hetero molecules

A: CC-Type2-II
B: CC-Type2-II
hetero molecules

A: CC-Type2-II
B: CC-Type2-II
hetero molecules

A: CC-Type2-II
B: CC-Type2-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,24712
Polymers25,8798
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area13860 Å2
ΔGint-134 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.110, 48.110, 126.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-101-

GOL

21A-132-

HOH

31A-135-

HOH

41A-136-

HOH

51A-137-

HOH

61A-138-

HOH

71B-225-

HOH

81B-229-

HOH

91B-230-

HOH

101B-231-

HOH

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Components

#1: Protein/peptide CC-Type2-II


Mass: 3234.871 Da / Num. of mol.: 2 / 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.: 69 / 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: 2.84 Å3/Da / Density % sol: 56.67 % / Mosaicity: 0.26 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Sodium citrate tribasic dihydrate, 50 mM Sodium cacodylate and 15% v/v 2-Propanol

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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 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.77→63.48 Å / Num. obs: 7676 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.021 / Rrim(I) all: 0.092 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.77-1.8119.20.8324140.9020.1930.855100
9.03-63.4814.60.051820.9960.0160.05499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.77 Å63.48 Å
Translation1.77 Å63.48 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→44.988 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2367 377 4.92 %
Rwork0.2037 --
obs0.2053 7661 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.65 Å2 / Biso mean: 30.7111 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 1.77→44.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms458 0 6 69 533
Biso mean--59.56 42.63 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008556
X-RAY DIFFRACTIONf_angle_d0.968770
X-RAY DIFFRACTIONf_chiral_restr0.04493
X-RAY DIFFRACTIONf_plane_restr0.00695
X-RAY DIFFRACTIONf_dihedral_angle_d13.156238
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
1.7702-2.02630.29041250.23323572482
2.0263-2.55290.24351320.209223882520
2.5529-45.00290.22411200.196625392659

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