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- PDB-6q5o: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Entry
Database: PDB / ID: 6q5o
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-LL
ComponentsCC-Hex*-LL
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / cc-hex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsRhys, G.G. / Wood, C.W. / Beesley, J.L. / 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 13, 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

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Assembly

Deposited unit
A: CC-Hex*-LL


Theoretical massNumber of molelcules
Total (without water)3,2361
Polymers3,2361
Non-polymers00
Water46826
1
A: CC-Hex*-LL

A: CC-Hex*-LL

A: CC-Hex*-LL

A: CC-Hex*-LL


Theoretical massNumber of molelcules
Total (without water)12,9444
Polymers12,9444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area6050 Å2
ΔGint-61 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.868, 29.378, 55.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

21A-121-

HOH

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Components

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


Mass: 3235.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.81 Å3/Da / Density % sol: 31.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.6 M potassium sodium tartrate tetrahydrate, 50 mM Tris

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.77999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77999 Å / Relative weight: 1
ReflectionResolution: 1→27.56 Å / Num. obs: 13041 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1-1.01712.84.4010.46430.451.8264.769100
2.714-27.5611.40.03461.87210.9990.0140.03799.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSBUILT20180808data reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→27.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.873 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21193 691 5.3 %RANDOM
Rwork0.16793 ---
obs0.17017 12350 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 19.543 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å2-0 Å20 Å2
2---0.38 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 1→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms226 0 0 26 252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013328
X-RAY DIFFRACTIONr_bond_other_d0.0010.017365
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.612453
X-RAY DIFFRACTIONr_angle_other_deg1.5211.592857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.611548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58427.7789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3721576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02378
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0258
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3571.628164
X-RAY DIFFRACTIONr_mcbond_other1.2691.6162
X-RAY DIFFRACTIONr_mcangle_it1.7262.436215
X-RAY DIFFRACTIONr_mcangle_other1.642.429215
X-RAY DIFFRACTIONr_scbond_it1.8512.026164
X-RAY DIFFRACTIONr_scbond_other1.832.021164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1672.831235
X-RAY DIFFRACTIONr_long_range_B_refined3.81619.851392
X-RAY DIFFRACTIONr_long_range_B_other3.50519.267386
X-RAY DIFFRACTIONr_rigid_bond_restr2.643693
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 58 -
Rwork0.398 886 -
obs--99.89 %

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