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- PDB-6g6f: Crystal structure of a parallel eight-helix coiled coil CC-Type2-LF -

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Basic information

Entry
Database: PDB / ID: 6g6f
TitleCrystal structure of a parallel eight-helix coiled coil CC-Type2-LF
ComponentsCC-Type2-LF
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 1.1Oct 23, 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-LF
B: CC-Type2-LF
C: CC-Type2-LF
D: CC-Type2-LF
E: CC-Type2-LF
F: CC-Type2-LF
G: CC-Type2-LF
H: CC-Type2-LF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0909
Polymers26,9678
Non-polymers1221
Water4,270237
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: equilibrium centrifugation, At the time of publication, solution-phase data indicated a heptameric species in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16290 Å2
ΔGint-164 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 58.990, 47.050
Angle α, β, γ (deg.)90.000, 109.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
CC-Type2-LF


Mass: 3370.935 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.04 Å3/Da / Density % sol: 39.76 % / Mosaicity: 0.26 °
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: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→58.99 Å / Num. obs: 22185 / % possible obs: 92.6 % / Redundancy: 5.7 % / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.012 / Rrim(I) all: 0.031 / Net I/σ(I): 36.7 / Num. measured all: 125674 / Scaling rejects: 215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.733.60.0797110.9910.0470.09356.4
9-58.995.90.0211790.9990.0090.02399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.1 Å44.45 Å
Translation5.1 Å44.45 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.452 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.1843 1085 4.9 %
Rwork0.156 --
obs0.1573 22164 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.78 Å2 / Biso mean: 18.19 Å2 / Biso min: 4.37 Å2
Refinement stepCycle: final / Resolution: 1.7→44.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 8 237 2156
Biso mean--42.62 30.69 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062049
X-RAY DIFFRACTIONf_angle_d0.7492741
X-RAY DIFFRACTIONf_chiral_restr0.034269
X-RAY DIFFRACTIONf_plane_restr0.004352
X-RAY DIFFRACTIONf_dihedral_angle_d16.851238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7002-1.77760.2943930.1851728182161
1.7776-1.87140.21411030.17742342244582
1.8714-1.98860.23041490.16162759290897
1.9886-2.14210.18471630.152128072970100
2.1421-2.35770.21061360.147328532989100
2.3577-2.69880.1941400.15628512991100
2.6988-3.40.1561400.161428552995100
3.4-44.46710.16171610.148828843045100

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