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- PDB-6g6h: Crystal structure of an antiparallel five-helix coiled coil 5H2L_... -

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Basic information

Entry
Database: PDB / ID: 6g6h
TitleCrystal structure of an antiparallel five-helix coiled coil 5H2L_2.1-I9L
Components5H2L_2.1-I9L
KeywordsDE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / AB_INITIO / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5H2L_2.1-I9L
B: 5H2L_2.1-I9L
C: 5H2L_2.1-I9L
D: 5H2L_2.1-I9L
E: 5H2L_2.1-I9L


Theoretical massNumber of molelcules
Total (without water)20,6715
Polymers20,6715
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, At the time of publication, solution-phase data indicated a tetrameric species in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-104 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.290, 65.320, 83.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
5H2L_2.1-I9L


Mass: 4134.103 Da / Num. of mol.: 5 / 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.: 131 / 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: 2.26 Å3/Da / Density % sol: 45.54 % / Mosaicity: 0.27 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM Potassium phosphate monobasic , 8% w/v PEG 8000 and 10% w/v Glycerol

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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: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.7→65.32 Å / Num. obs: 21295 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.036 / Rrim(I) all: 0.113 / Net I/σ(I): 14.4 / Num. measured all: 219288 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.739.91.36310910.7410.4711.44498.7
9-65.329.40.0411880.9980.0130.04399.8

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Phasing

PhasingMethod: AB_INITIO

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
Arcimboldo4.0.0phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.7→51.417 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2301 1025 4.83 %
Rwork0.1834 --
obs0.1857 21205 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.7 Å2 / Biso mean: 27.2098 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: final / Resolution: 1.7→51.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 131 1575
Biso mean---41.63 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061490
X-RAY DIFFRACTIONf_angle_d0.7471968
X-RAY DIFFRACTIONf_chiral_restr0.037232
X-RAY DIFFRACTIONf_plane_restr0.003231
X-RAY DIFFRACTIONf_dihedral_angle_d19.2071020
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.78960.25891320.20562797292998
1.7896-1.90180.22541380.2042829296799
1.9018-2.04860.24791550.190328352990100
2.0486-2.25480.26261600.180528473007100
2.2548-2.5810.23211280.18228943022100
2.581-3.25170.21411520.191529133065100
3.2517-51.44090.22161600.173630653225100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78950.24120.12760.47680.57510.67540.1237-0.18390.19870.5056-0.15520.0702-0.4448-0.10490.10710.1954-0.0469-0.0130.1567-0.03520.1298-0.0542-0.908314.6436
20.53870.23720.36580.94260.79010.6140.1547-0.11180.36080.1024-0.17640.6831-0.314-0.2247-0.24950.1015-0.01560.05910.2037-0.04270.2134-7.7512-3.11969.734
30.4033-0.1254-0.03410.92460.5010.4484-0.02610.1090.0641-0.2340.00520.17540.212-0.3032-0.03160.1269-0.03620.00250.154-0.01980.15-5.6233-10.11542.9982
40.44620.27160.63710.15170.31570.7026-0.1124-0.0763-0.137-0.5008-0.1152-0.28040.46320.18280.20720.13290.03080.05890.13740.03130.16343.6154-12.36874.3719
50.16740.06540.26950.33130.55050.78470.0917-0.1374-0.02710.2249-0.3167-0.435-0.0240.4049-0.00870.1182-0.007-0.03070.21110.06870.21187.288-7.078211.9976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A1 - 33
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 33 )B1 - 33
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 33 )C1 - 33
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 33 )D1 - 33
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 33 )E1 - 33

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