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- PDB-6eiz: A de novo designed hexameric coiled coil CC-Hex2 with farnesol bo... -

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Basic information

Entry
Database: PDB / ID: 6eiz
TitleA de novo designed hexameric coiled coil CC-Hex2 with farnesol bound in the channel.
ComponentsCC-Hex2
KeywordsDE NOVO PROTEIN / Alpha-Helical Coiled-Coil Barrel
Function / homology(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRhys, G.G. / Burton, A.J. / Dawson, W.M. / Thomas, F. / Woolfson, D.N.
Funding support United Kingdom, Belgium, 5items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2012- 536 United Kingdom
European Research Council340764 Belgium
Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research CouncilBB/L01386X1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K03927X/1 United Kingdom
CitationJournal: ACS Synth Biol / Year: 2018
Title: De Novo-Designed alpha-Helical Barrels as Receptors for Small Molecules.
Authors: Thomas, F. / Dawson, W.M. / Lang, E.J.M. / Burton, A.J. / Bartlett, G.J. / Rhys, G.G. / Mulholland, A.J. / Woolfson, D.N.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Feb 20, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-Hex2
B: CC-Hex2
C: CC-Hex2
D: CC-Hex2
E: CC-Hex2
F: CC-Hex2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0287
Polymers19,8066
Non-polymers2221
Water2,756153
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-74 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.080, 126.230, 58.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide
CC-Hex2


Mass: 3300.973 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FOF / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / trans,trans-Farnesol


Mass: 222.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Na HEPES, 4.3 M Sodium Chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→26.345 Å / Num. all: 218674 / Num. obs: 19015 / % possible obs: 92.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.036 / Net I/σ(I): 10.5
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 19015 / CC1/2: 0.934 / Rpim(I) all: 0.416 / % possible all: 57

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pn8

4pn8


Resolution: 1.85→26.345 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 861 4.9 %Random
Rwork0.221 ---
obs0.2229 17574 92.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→26.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 16 153 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081392
X-RAY DIFFRACTIONf_angle_d1.0831839
X-RAY DIFFRACTIONf_dihedral_angle_d13.77561
X-RAY DIFFRACTIONf_chiral_restr0.04217
X-RAY DIFFRACTIONf_plane_restr0.005204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-1.96610.3142760.30781710X-RAY DIFFRACTION57
1.9661-2.11780.33241550.2962891X-RAY DIFFRACTION98
2.1178-2.33080.31451640.24442975X-RAY DIFFRACTION100
2.3308-2.66780.28981360.23863006X-RAY DIFFRACTION100
2.6678-3.36010.26061550.20133011X-RAY DIFFRACTION100
3.3601-26.34760.21131750.19233120X-RAY DIFFRACTION100
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)
13.5391-0.30490.298.971-4.00724.51910.0297-0.0329-0.034-0.04520.09370.94610.0483-0.1931-0.12450.0782-0.02780.0020.2265-0.03560.114168.7831401.0959119.4698
21.9862-0.946-0.87486.66581.25762.9395-0.0335-0.5155-0.17740.8189-0.05010.20390.213-0.04770.07240.1512-0.06440.00630.39520.05680.120273.7691400.0452126.9194
32.8744-1.5757-0.11678.03331.44023.07940.2216-1.2415-0.09510.7038-0.0695-0.3920.29880.677-0.14160.12360.0286-0.07470.69090.23980.106682.5713400.1406126.2884
42.1947-0.2264-0.24035.57981.51171.91340.09-0.5741-0.1466-0.09680.0181-0.70520.18240.71-0.07010.13190.11220.00790.67980.14810.220986.678400.66118.4015
54.31334.8490.952.07011.85162.6149-0.07690.0584-0.0101-0.4796-0.0349-0.21850.19580.88250.05850.22440.17040.0190.50370.07590.202781.8854401.8647110.9165
63.66723.138-0.05198.0706-0.71352.5879-0.04880.39790.0598-0.5366-0.00820.40030.27080.44060.09870.21090.0821-0.02450.1642-0.02980.131472.7741401.5045111.4258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 29 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 30 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 30 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 30 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 29 )

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