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- PDB-6q5p: Crystal structure of a CC-Hex mutant that forms a parallel six-he... -

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Basic information

Entry
Database: PDB / ID: 6q5p
TitleCrystal structure of a CC-Hex mutant that forms a parallel six-helix coiled coil CC-Hex*-II
ComponentsCC-Hex*-II
KeywordsDE NOVO PROTEIN / coiled coil / hexamer / synthetic / parallel / cc-hex
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hex*-II
B: CC-Hex*-II
C: CC-Hex*-II
D: CC-Hex*-II
E: CC-Hex*-II
F: CC-Hex*-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6919
Polymers19,4096
Non-polymers2823
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-113 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.763, 62.763, 82.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-101-

PO4

21A-101-

PO4

31A-208-

HOH

41A-217-

HOH

51F-132-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 30
2010B1 - 30
1020A1 - 30
2020C1 - 30
1030A1 - 30
2030D1 - 30
1040A1 - 30
2040E1 - 30
1050A1 - 30
2050F1 - 30
1060B1 - 30
2060C1 - 30
1070B1 - 30
2070D1 - 30
1080B1 - 30
2080E1 - 30
1090B1 - 30
2090F1 - 30
10100C1 - 30
20100D1 - 30
10110C1 - 30
20110E1 - 30
10120C1 - 30
20120F1 - 30
10130D1 - 30
20130E1 - 30
10140D1 - 30
20140F1 - 30
10150E1 - 30
20150F1 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 3234.871 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM SPG buffer (succinic acid, sodium phosphate monobasic monohydrate, glycine), 25 % w/v PEG1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9163 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: 0.9163 Å / Relative weight: 1
ReflectionResolution: 1.44→82.61 Å / Num. obs: 33440 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 16.501 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.047 / Rrim(I) all: 0.151 / Χ2: 0.91 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.44-1.48193.7121.124610.5371.2653.9230.83
6.44-82.6119.40.04749.13980.9990.0150.0490.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.11.4-g9c616a499-releasedata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→54.41 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.653 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17064 1680 5 %RANDOM
Rwork0.16449 ---
obs0.16484 31709 99.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 23.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.44→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 16 185 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181596
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6292028
X-RAY DIFFRACTIONr_angle_other_deg1.4841.5883721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.415196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53426.85254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73515325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
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_it2.5331.395780
X-RAY DIFFRACTIONr_mcbond_other2.5131.387778
X-RAY DIFFRACTIONr_mcangle_it3.2212.039980
X-RAY DIFFRACTIONr_mcangle_other3.2272.038980
X-RAY DIFFRACTIONr_scbond_it4.171.767730
X-RAY DIFFRACTIONr_scbond_other4.1411.761727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0372.4671043
X-RAY DIFFRACTIONr_long_range_B_refined7.22419.1521947
X-RAY DIFFRACTIONr_long_range_B_other7.22219.1741948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8220.13
12B8220.13
21A8120.16
22C8120.16
31A8050.14
32D8050.14
41A8230.13
42E8230.13
51A8260.13
52F8260.13
61B8520.14
62C8520.14
71B8540.13
72D8540.13
81B8540.12
82E8540.12
91B8570.12
92F8570.12
101C9310.09
102D9310.09
111C8870.13
112E8870.13
121C9020.13
122F9020.13
131D8120.15
132E8120.15
141D8130.13
142F8130.13
151E9670.08
152F9670.08
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 122 -
Rwork0.301 2319 -
obs--99.55 %
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)
11.5241-0.32630.49351.82352.39735.7262-0.081-0.2179-0.01560.1201-0.01650.05080.17910.04170.09750.03120.0028-0.00710.06230.0040.032823.702-12.493-12.695
21.7152-0.64091.14080.53330.54296.4876-0.0772-0.03510.23840.0294-0.0913-0.06370.04860.08370.16850.01770.01410.00470.1128-0.0280.107631.291-7.916-17.491
31.6730.05381.77741.45532.98058.55620.0868-0.0772-0.0508-0.02480.0170.05990.10090.0127-0.10380.02870.0014-0.01450.0379-0.01010.042915.332-9.528-21.276
42.0079-0.00432.48431.11881.58367.36570.0034-0.07190.2778-0.0554-0.0842-0.0797-0.05140.02030.08080.0251-0.00790.0170.0442-0.03090.069324.167-2.282-20.013
52.39130.71923.21561.6152.32087.1286-0.0342-0.0560.2847-0.0447-0.01290.0112-0.1016-0.00560.04720.04680.00830.00210.0275-0.02490.086215.9062.909-21.636
63.03671.11372.4511.90323.26396.23470.0578-0.29730.0653-0.07130.01770.0741-0.0227-0.1883-0.07560.0401-0.0119-0.03990.12360.03720.10038.374-2.826-18.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E1 - 30
6X-RAY DIFFRACTION6F1 - 30

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