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- PDB-6q5k: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

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Basic information

Entry
Database: PDB / ID: 6q5k
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-L24K
ComponentsCC-Hex*-L24K
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: 1.65 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*-L24K
B: CC-Hex*-L24K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7266
Polymers6,5022
Non-polymers2244
Water57632
1
A: CC-Hex*-L24K
B: CC-Hex*-L24K
hetero molecules

A: CC-Hex*-L24K
B: CC-Hex*-L24K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,45212
Polymers13,0044
Non-polymers4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area5880 Å2
ΔGint-71 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 69.280, 35.441
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
11B-101-

NH4

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Components

#1: Protein/peptide CC-Hex*-L24K


Mass: 3250.893 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.05 M Tris, 0.75 M ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→24.78 Å / Num. obs: 6134 / % possible obs: 96.5 % / Redundancy: 20.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.018 / Rrim(I) all: 0.073 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.6818.81.3562.72690.6820.3161.393100
9.04-24.7814.50.02950.45310.0080.0395.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PHASER7.0.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→24.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.649 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21834 313 5.1 %RANDOM
Rwork0.17174 ---
obs0.17395 5821 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.65→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 13 32 445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013441
X-RAY DIFFRACTIONr_bond_other_d0.0020.017474
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.639588
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5931107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.409555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14525.62516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3915100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02467
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0269
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_it2.0712.184221
X-RAY DIFFRACTIONr_mcbond_other2.0642.162220
X-RAY DIFFRACTIONr_mcangle_it3.3843.192277
X-RAY DIFFRACTIONr_mcangle_other3.3833.217278
X-RAY DIFFRACTIONr_scbond_it2.4542.687220
X-RAY DIFFRACTIONr_scbond_other2.452.695221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.733.855312
X-RAY DIFFRACTIONr_long_range_B_refined6.41726.041520
X-RAY DIFFRACTIONr_long_range_B_other6.41126.119521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 22 -
Rwork0.29 390 -
obs--89.76 %
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)
12.61232.42082.00523.22551.81333.011-0.26680.19760.0399-0.07010.0548-0.052-0.06160.40050.21190.1172-0.01020.00360.12450.03160.0489-8.922-31.454-6.476
20.99462.3205-0.55047.0907-0.81430.6093-0.09070.1110.0288-0.00040.05120.0955-0.0091-0.14870.03950.1147-0.0138-0.03140.0633-0.0040.0157-18.168-23.7740.457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 24
2X-RAY DIFFRACTION2B1 - 27

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