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- PDB-6q5h: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Basic information

Entry
Database: PDB / ID: 6q5h
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-L24D
ComponentsCC-Hex*-L24D
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / cc-hex
Function / homologyAMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWood, C.W. / Beesley, J.L. / Rhys, G.G. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hex*-L24D
B: CC-Hex*-L24D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7026
Polymers6,4742
Non-polymers2284
Water1,00956
1
A: CC-Hex*-L24D
B: CC-Hex*-L24D
hetero molecules

A: CC-Hex*-L24D
B: CC-Hex*-L24D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,40412
Polymers12,9474
Non-polymers4568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area5540 Å2
ΔGint-103 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.200, 70.200, 35.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-101-

NH4

21A-204-

HOH

31A-234-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 23
2010B1 - 23

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Components

#1: Protein/peptide CC-Hex*-L24D


Mass: 3236.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.95 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.0 M Ammonium sulfate, 0.05 M Tris.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→15.87 Å / Num. obs: 16641 / % possible obs: 99.9 % / Redundancy: 36.3 % / Biso Wilson estimate: 17.741 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.022 / Rrim(I) all: 0.016 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.2334.34.04912150.7280.6974.1199.9
5.37-15.8730.30.03922810.0070.03996.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSNov 11, 2017data reduction
XDSNov 11, 2017data scaling
PHASER7.0.052phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→15.87 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.262 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17979 843 5.1 %RANDOM
Rwork0.15097 ---
obs0.15252 15774 99.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 46.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.2→15.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms403 0 12 56 471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.015450
X-RAY DIFFRACTIONr_bond_other_d0.0010.017467
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.679606
X-RAY DIFFRACTIONr_angle_other_deg1.161.671092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.641558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97626.11118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4141598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.263
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0271
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_it43.9853.891227
X-RAY DIFFRACTIONr_mcbond_other38.2153.803226
X-RAY DIFFRACTIONr_mcangle_it57.6275.545285
X-RAY DIFFRACTIONr_mcangle_other57.6825.733286
X-RAY DIFFRACTIONr_scbond_it40.9894.786223
X-RAY DIFFRACTIONr_scbond_other41.6314.844216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other33.5436.462309
X-RAY DIFFRACTIONr_long_range_B_refined49.0243.297531
X-RAY DIFFRACTIONr_long_range_B_other47.742.415514
X-RAY DIFFRACTIONr_rigid_bond_restr30.6853917
X-RAY DIFFRACTIONr_sphericity_free33.421532
X-RAY DIFFRACTIONr_sphericity_bonded97.6215939
Refine LS restraints NCS

Ens-ID: 1 / Number: 649 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 65 -
Rwork0.405 1148 -
obs--99.92 %

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