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- PDB-6zt1: Two states of a de novo hexameric coiled coil assembly CC-Type2-(... -

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Basic information

Entry
Database: PDB / ID: 6zt1
TitleTwo states of a de novo hexameric coiled coil assembly CC-Type2-(LaIdGe)4
ComponentsCC-Type2-(LaIdGe)4
KeywordsDE NOVO PROTEIN / coiled coil / de novo peptide / multi-state
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
CitationJournal: Nat Commun / Year: 2021
Title: Structural resolution of switchable states of a de novo peptide assembly.
Authors: Dawson, W.M. / Lang, E.J.M. / Rhys, G.G. / Shelley, K.L. / Williams, C. / Brady, R.L. / Crump, M.P. / Mulholland, A.J. / Woolfson, D.N.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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-Type2-(LaIdGe)4
B: CC-Type2-(LaIdGe)4
C: CC-Type2-(LaIdGe)4
D: CC-Type2-(LaIdGe)4
E: CC-Type2-(LaIdGe)4
F: CC-Type2-(LaIdGe)4
G: CC-Type2-(LaIdGe)4
H: CC-Type2-(LaIdGe)4
I: CC-Type2-(LaIdGe)4
J: CC-Type2-(LaIdGe)4
K: CC-Type2-(LaIdGe)4
L: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)38,62412
Polymers38,62412
Non-polymers00
Water2,684149
1
A: CC-Type2-(LaIdGe)4
B: CC-Type2-(LaIdGe)4
C: CC-Type2-(LaIdGe)4
D: CC-Type2-(LaIdGe)4
E: CC-Type2-(LaIdGe)4
F: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)19,3126
Polymers19,3126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-87 kcal/mol
Surface area9770 Å2
MethodPISA
2
G: CC-Type2-(LaIdGe)4
H: CC-Type2-(LaIdGe)4
I: CC-Type2-(LaIdGe)4
J: CC-Type2-(LaIdGe)4
K: CC-Type2-(LaIdGe)4
L: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)19,3126
Polymers19,3126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-104 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 128.100, 56.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name N or name...
21(chain B and ((resid 3 and (name N or name...
31(chain C and ((resid 3 and (name N or name...
41(chain D and ((resid 3 and (name N or name...
51(chain E and ((resid 3 and (name N or name...
61(chain F and ((resid 3 and (name N or name...
71(chain G and ((resid 3 and (name O or name...
81(chain H and ((resid 3 and (name N or name...
91(chain J and ((resid 3 and (name N or name...
101(chain K and ((resid 3 and (name O or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 3 and (name N or name...A3
121(chain A and ((resid 3 and (name N or name...A0 - 30
131(chain A and ((resid 3 and (name N or name...A0 - 30
141(chain A and ((resid 3 and (name N or name...A0 - 30
151(chain A and ((resid 3 and (name N or name...A0 - 30
161(chain A and ((resid 3 and (name N or name...A0 - 30
211(chain B and ((resid 3 and (name N or name...B3
221(chain B and ((resid 3 and (name N or name...B0 - 30
231(chain B and ((resid 3 and (name N or name...B0 - 30
241(chain B and ((resid 3 and (name N or name...B0 - 30
251(chain B and ((resid 3 and (name N or name...B0 - 30
261(chain B and ((resid 3 and (name N or name...B0 - 30
311(chain C and ((resid 3 and (name N or name...C3
321(chain C and ((resid 3 and (name N or name...C0 - 30
331(chain C and ((resid 3 and (name N or name...C0 - 30
341(chain C and ((resid 3 and (name N or name...C0 - 30
351(chain C and ((resid 3 and (name N or name...C0 - 30
361(chain C and ((resid 3 and (name N or name...C0 - 30
411(chain D and ((resid 3 and (name N or name...D3
421(chain D and ((resid 3 and (name N or name...D0 - 30
431(chain D and ((resid 3 and (name N or name...D0 - 30
441(chain D and ((resid 3 and (name N or name...D0 - 30
451(chain D and ((resid 3 and (name N or name...D0 - 30
461(chain D and ((resid 3 and (name N or name...D0 - 30
511(chain E and ((resid 3 and (name N or name...E3
521(chain E and ((resid 3 and (name N or name...E0 - 29
531(chain E and ((resid 3 and (name N or name...E0 - 29
541(chain E and ((resid 3 and (name N or name...E0 - 29
551(chain E and ((resid 3 and (name N or name...E0 - 29
561(chain E and ((resid 3 and (name N or name...E0 - 29
611(chain F and ((resid 3 and (name N or name...F3
621(chain F and ((resid 3 and (name N or name...F0 - 30
631(chain F and ((resid 3 and (name N or name...F0 - 30
641(chain F and ((resid 3 and (name N or name...F0 - 30
651(chain F and ((resid 3 and (name N or name...F0 - 30
661(chain F and ((resid 3 and (name N or name...F0 - 30
711(chain G and ((resid 3 and (name O or name...G3
721(chain G and ((resid 3 and (name O or name...G2 - 30
731(chain G and ((resid 3 and (name O or name...G2 - 30
741(chain G and ((resid 3 and (name O or name...G2 - 30
751(chain G and ((resid 3 and (name O or name...G2 - 30
761(chain G and ((resid 3 and (name O or name...G2 - 30
811(chain H and ((resid 3 and (name N or name...H3
821(chain H and ((resid 3 and (name N or name...H1 - 30
831(chain H and ((resid 3 and (name N or name...H1 - 30
841(chain H and ((resid 3 and (name N or name...H1 - 30
851(chain H and ((resid 3 and (name N or name...H1 - 30
861(chain H and ((resid 3 and (name N or name...H1 - 30
911(chain J and ((resid 3 and (name N or name...J3
921(chain J and ((resid 3 and (name N or name...J0 - 30
931(chain J and ((resid 3 and (name N or name...J0 - 30
941(chain J and ((resid 3 and (name N or name...J0 - 30
951(chain J and ((resid 3 and (name N or name...J0 - 30
961(chain J and ((resid 3 and (name N or name...J0 - 30
1011(chain K and ((resid 3 and (name O or name...K3
1021(chain K and ((resid 3 and (name O or name...K1 - 29
1031(chain K and ((resid 3 and (name O or name...K1 - 29
1041(chain K and ((resid 3 and (name O or name...K1 - 29
1051(chain K and ((resid 3 and (name O or name...K1 - 29
1061(chain K and ((resid 3 and (name O or name...K1 - 29

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Components

#1: Protein/peptide
CC-Type2-(LaIdGe)4


Mass: 3218.627 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M Sodium HEPES, 5% w/v PEG 4000 and 5% v/v 2-Propanol at a pH of 7 (values based on 1:1 dilution of ProPlex B6 crystallisation condition with peptide solution)

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.01→58.92 Å / Num. obs: 29226 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
2.01-2.0813.31.6381.828760.5650.8580.4651.70499.9
8.99-58.929.80.05729.83860.0190.0696.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→56.53 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1396 4.78 %
Rwork0.2071 --
obs0.2097 29204 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.77 Å2 / Biso mean: 45.6945 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 2.01→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 149 2785
Biso mean---51.69 -
Num. residues----364
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A291X-RAY DIFFRACTION11.478TORSIONAL
12B291X-RAY DIFFRACTION11.478TORSIONAL
13C291X-RAY DIFFRACTION11.478TORSIONAL
14D291X-RAY DIFFRACTION11.478TORSIONAL
15E291X-RAY DIFFRACTION11.478TORSIONAL
16F291X-RAY DIFFRACTION11.478TORSIONAL
17G291X-RAY DIFFRACTION11.478TORSIONAL
18H291X-RAY DIFFRACTION11.478TORSIONAL
19J291X-RAY DIFFRACTION11.478TORSIONAL
110K291X-RAY DIFFRACTION11.478TORSIONAL
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)
10.1642-0.41260.10561.81430.51310.8674-0.4673-0.157-0.11461.51660.73850.96980.016-0.20380.01850.4410.11950.09040.39420.07030.261525.400741.47486.3684
21.20440.549-0.09990.3153-0.06580.1292-0.01010.08250.18820.10610.31610.6450.0203-0.15640.00480.33220.00640.00620.38890.07450.319518.962941.8192-0.7766
3-0.3520.86890.54350.59710.72190.499-0.42620.10580.3272-1.25120.67761.00950.2111-0.22270.00110.3564-0.0301-0.0260.42840.07340.383821.919842.0121-9.3143
40.3411-0.2473-0.37221.2453-0.1930.7957-0.42460.0727-0.2626-0.84920.6082-1.11740.0006-0.00590.00910.321-0.04740.02350.3765-0.00580.269430.987541.19-11.7317
52.07910.3738-0.56951.0039-0.64590.3695-0.22520.049-0.2233-0.50740.4463-1.4686-0.09890.2545-0.00090.33290.07960.00880.346-0.020.332937.609841.0198-4.0926
6-0.25790.67080.12921.5592-0.95620.5573-0.2663-0.23370.01431.63060.3748-0.60960.02550.1030.00140.38580.1022-0.05070.386-0.01560.371634.74441.01234.5904
71.9716-1.13960.68950.9111-0.15250.8477-0.06540.4216-0.2645-1.0010.255-0.06410.02820.04110.00450.37360.0147-0.00580.3377-0.06840.333127.968123.162618.6184
82.9213-0.75410.56033.47131.65891.82860.35280.3881-0.301-1.5206-0.2632-0.5248-0.51870.0353-0.04330.23610.03070.05220.2785-0.1020.329135.789722.853622.1296
92.28950.2407-0.14330.9197-0.98330.98590.37270.0418-0.11730.1809-0.1722-1.54840.0810.0847-0.0050.25450.0126-0.05650.2834-0.02570.408738.630721.943730.0571
102.06691.08840.62970.70180.6860.99890.0833-0.5002-0.20171.0310.0153-0.18460.1088-0.06650.00640.3378-0.0207-0.00360.24550.04880.285827.771523.563632.5873
111.4655-0.10130.11110.2320.04240.96140.2122-0.2302-0.26840.1912-0.00811.23970.0829-0.19430.0010.2957-0.0503-0.02140.31130.0650.402720.688722.618527.6837
124.45840.7660.95630.7710.65781.13120.5120.1645-0.15150.25430.02351.5688-0.1023-0.32070.04030.31390.0068-0.04180.3246-0.02220.429417.571922.674120.4207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A1 - 30
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 30 )B1 - 30
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 30 )C1 - 30
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 30 )D1 - 30
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 29 )E1 - 29
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 30 )F1 - 30
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 30 )G2 - 30
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 30 )H1 - 30
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 30 )I1 - 30
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 30 )J1 - 30
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 29 )K1 - 29
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 29 )L1 - 29

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