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- PDB-6g6e: Crystal structure of a parallel seven-helix coiled coil CC-Type2-deLI -

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Basic information

Entry
Database: PDB / ID: 6g6e
TitleCrystal structure of a parallel seven-helix coiled coil CC-Type2-deLI
ComponentsCC-Type2-deLI
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: 1.26 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 1.1Apr 9, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-deLI
B: CC-Type2-deLI
C: CC-Type2-deLI
D: CC-Type2-deLI
E: CC-Type2-deLI
F: CC-Type2-deLI
G: CC-Type2-deLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,04812
Polymers22,5887
Non-polymers4605
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-81 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.201, 47.950, 129.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11G-101-

HOH

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Components

#1: Protein/peptide
CC-Type2-deLI


Mass: 3226.807 Da / Num. of mol.: 7 / 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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.93 Å3/Da / Density % sol: 36.22 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Magnesium Chloride hexahydrate, 50 mM Sodium HEPES and 15% w/v PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.26→64.67 Å / Num. obs: 65209 / % possible obs: 99.9 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.02 / Rrim(I) all: 0.067 / Net I/σ(I): 15.5 / Num. measured all: 746680 / Scaling rejects: 239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.26-1.289.91.11931760.8350.3691.1899.5
6.9-64.6710.10.074850.9930.0250.07599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.26 Å64.67 Å
Translation1.26 Å64.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→64.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.086 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3271 5 %RANDOM
Rwork0.1805 ---
obs0.1815 61872 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 22.505 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---0.16 Å20 Å2
3----2.16 Å2
Refinement stepCycle: final / Resolution: 1.26→64.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 30 171 1800
Biso mean--53.28 40.87 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0181974
X-RAY DIFFRACTIONr_bond_other_d0.0030.0232176
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.8912584
X-RAY DIFFRACTIONr_angle_other_deg0.9041.9675024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4345210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.27523.37837
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36915255
X-RAY DIFFRACTIONr_chiral_restr0.1160.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 224 -
Rwork0.368 4509 -
all-4733 -
obs--99.41 %

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