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- PDB-6q5r: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Basic information

Entry
Database: PDB / ID: 6q5r
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-LL-KgEb
ComponentsCC-Hex*-LL-KgEb
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / cc-hex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsBeesley, J.L. / Rhys, G.G. / Wood, C.W. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, Belgium, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 Belgium
Biotechnology and Biological Sciences Research CouncilBB/R00661X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K03927X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles.
Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: 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
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-Hex*-LL-KgEb
B: CC-Hex*-LL-KgEb
C: CC-Hex*-LL-KgEb
D: CC-Hex*-LL-KgEb
E: CC-Hex*-LL-KgEb
F: CC-Hex*-LL-KgEb
G: CC-Hex*-LL-KgEb
H: CC-Hex*-LL-KgEb
I: CC-Hex*-LL-KgEb
J: CC-Hex*-LL-KgEb
K: CC-Hex*-LL-KgEb
L: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00314
Polymers38,81812
Non-polymers1842
Water4,972276
1
A: CC-Hex*-LL-KgEb
B: CC-Hex*-LL-KgEb
C: CC-Hex*-LL-KgEb
D: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,9394
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-65 kcal/mol
Surface area6920 Å2
MethodPISA
2
E: CC-Hex*-LL-KgEb
F: CC-Hex*-LL-KgEb
G: CC-Hex*-LL-KgEb
H: CC-Hex*-LL-KgEb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,9394
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-65 kcal/mol
Surface area6870 Å2
MethodPISA
3
I: CC-Hex*-LL-KgEb
J: CC-Hex*-LL-KgEb
K: CC-Hex*-LL-KgEb
L: CC-Hex*-LL-KgEb


Theoretical massNumber of molelcules
Total (without water)12,9394
Polymers12,9394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-65 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.626, 46.748, 48.162
Angle α, β, γ (deg.)88.70, 61.70, 81.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
CC-Hex*-LL-KgEb


Mass: 3234.871 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.63 M ammonium sulfate, 0.1 M lithium sulfate, 50 mM Tris

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.61→42.34 Å / Num. obs: 43409 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.89 Å2 / CC1/2: 0.945 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.173 / Rrim(I) all: 0.244 / Χ2: 0.75 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.61-1.650.9872.631300.5030.9871.3960.695.4
7.2-42.340.2368.85000.9270.2360.3342.2899.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALS1.10.3data reduction
Aimless0.5.32data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→39.974 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 2076 4.79 %RANDOM
Rwork0.1958 ---
obs0.1977 43308 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→39.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 12 276 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052884
X-RAY DIFFRACTIONf_angle_d0.7773866
X-RAY DIFFRACTIONf_dihedral_angle_d1.7172321
X-RAY DIFFRACTIONf_chiral_restr0.031461
X-RAY DIFFRACTIONf_plane_restr0.004470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.64740.28051270.21782551X-RAY DIFFRACTION91
1.6474-1.68860.25161440.22452699X-RAY DIFFRACTION95
1.6886-1.73430.25461470.22822718X-RAY DIFFRACTION95
1.7343-1.78530.2761290.22392736X-RAY DIFFRACTION96
1.7853-1.8430.25931380.21832713X-RAY DIFFRACTION96
1.843-1.90880.2321410.19872725X-RAY DIFFRACTION96
1.9088-1.98520.23491500.20272753X-RAY DIFFRACTION97
1.9852-2.07560.26381330.19282790X-RAY DIFFRACTION97
2.0756-2.1850.22111500.1852760X-RAY DIFFRACTION97
2.185-2.32190.24091500.19072739X-RAY DIFFRACTION97
2.3219-2.50120.23441390.19182784X-RAY DIFFRACTION98
2.5012-2.75280.21021430.1812805X-RAY DIFFRACTION98
2.7528-3.1510.23511430.1972790X-RAY DIFFRACTION98
3.151-3.96940.19371010.17872857X-RAY DIFFRACTION99
3.9694-39.98580.26071410.20292812X-RAY DIFFRACTION99
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)
11.2289-1.7227-1.39796.33684.32944.39-0.05350.04170.02620.30230.2823-0.7030.16660.1062-0.1110.0683-0.0135-0.0150.13230.01440.1892.7556-3.9662-0.7364
21.29821.2670.03165.34941.20811.5554-0.10170.09070.0338-0.1431-0.00510.7364-0.0979-0.02860.1020.0471-0.0097-0.00950.12290.01410.1387-10.8748-2.4259-1.1214
32.4117-2.2948-1.18255.54512.43272.01440.0160.02020.03730.6816-0.0389-0.35030.06420.0138-0.04560.0823-0.02770.0060.10370.02520.0708-6.497-2.34795.9314
41.79591.44290.2274.01241.30361.3948-0.18670.2556-0.098-0.71670.4954-0.9577-0.21530.1203-0.07790.1578-0.03510.06290.11830.03380.1266-1.5491.1089-5.9484
52.82731.8111.40972.34022.32133.1861-0.19650.06140.0565-0.58530.28510.0158-0.19660.0719-0.10890.087-0.02320.00380.12260.0270.0999-29.4179-4.9599-8.0605
63.4546-3.9044-1.12745.27232.62593.0185-0.2715-0.3578-0.04280.57650.4421-0.31730.0910.2369-0.12590.10630.0167-0.0050.18650.03080.1279-24.177-7.85583.9481
72.19491.94181.29055.91634.31484.933-0.2508-0.02210.0422-0.46880.5429-0.4578-0.22770.439-0.1380.08330.00540.00240.14020.00640.1673-20.213-3.7778-1.5273
81.7527-1.51370.05831.83070.94721.9253-0.1420.0379-0.0589-0.10950.18040.61140.0804-0.04040.03140.0562-0.00920.00240.11030.01680.1649-33.4635-4.512-1.012
91.0989-0.0374-0.72241.242-0.83681.746-0.09910.0916-0.002-0.51990.11770.2792-0.0811-0.16930.01420.1924-0.0335-0.0270.14360.03160.0792-18.8095-2.435514.9492
100.81680.136-0.67893.79553.84044.6196-0.194-0.0311-0.0568-0.08870.3066-0.5156-0.15570.258-0.01790.2364-0.0192-0.02630.11940.04640.1368-11.1768-4.959726.1309
110.62080.153-0.01824.0944-0.85951.32120.0104-0.0552-0.0450.65210.01870.68420.0129-0.1414-0.09230.2388-0.03120.03050.13190.03510.0829-18.7502-7.578925.0529
120.70810.29581.28832.98912.67613.61230.0265-0.0086-0.0775-0.19510.07-0.5825-0.026-0.0874-0.09720.2097-0.04740.06580.10530.00930.1047-11.0501-4.975814.2658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:30)
2X-RAY DIFFRACTION2(chain B and resseq 1:30)
3X-RAY DIFFRACTION3(chain C and resseq 1:30)
4X-RAY DIFFRACTION4(chain D and resseq 1:30)
5X-RAY DIFFRACTION5(chain E and resseq 1:30)
6X-RAY DIFFRACTION6(chain F and resseq 1:30)
7X-RAY DIFFRACTION7(chain G and resseq 1:30)
8X-RAY DIFFRACTION8(chain H and resseq 1:30)
9X-RAY DIFFRACTION9(chain I and resseq 1:30)
10X-RAY DIFFRACTION10(chain J and resseq 1:30)
11X-RAY DIFFRACTION11(chain K and resseq 1:30)
12X-RAY DIFFRACTION12(chain L and resseq 1:30)

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