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- PDB-7a1t: A collapsed hexameric state of a de novo coiled-coil assembly: CC... -

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Basic information

Entry
Database: PDB / ID: 7a1t
TitleA collapsed hexameric state of a de novo coiled-coil assembly: CC-Type2-(GgLaId)4-W19BrPhe.
ComponentsCC-Type2-(GgLaId)4-W19BrPhe
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Function / homologyACETATE ION / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
CitationJournal: Chem Sci / Year: 2021
Title: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states.
Authors: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / Woolfson, D.N.
History
DepositionAug 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CC-Type2-(GgLaId)4-W19BrPhe
B: CC-Type2-(GgLaId)4-W19BrPhe
C: CC-Type2-(GgLaId)4-W19BrPhe
D: CC-Type2-(GgLaId)4-W19BrPhe
E: CC-Type2-(GgLaId)4-W19BrPhe
F: CC-Type2-(GgLaId)4-W19BrPhe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,75212
Polymers19,3126
Non-polymers4416
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-108 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.646, 129.687, 59.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-213-

HOH

21D-214-

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 - 28
2030D1 - 28
1040A1 - 30
2040E1 - 30
1050A1 - 30
2050F1 - 30
1060B1 - 30
2060C1 - 30
1070B1 - 28
2070D1 - 28
1080B1 - 30
2080E1 - 30
1090B1 - 30
2090F1 - 30
10100C1 - 28
20100D1 - 28
10110C1 - 30
20110E1 - 30
10120C1 - 30
20120F1 - 30
10130D1 - 28
20130E1 - 28
10140D1 - 28
20140F1 - 28
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-Type2-(GgLaId)4-W19BrPhe


Mass: 3218.627 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM sodium HEPES buffer, 500 mM sodium acetate and 25 mM cadmium sulfate (8/3)-hydrate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I04 / Wavelength: 0.9187 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 1.42→59.12 Å / Num. obs: 37216 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 18.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.42-1.4612.92.471.127210.5020.7092.572100
6.35-59.1211.30.06346.94820.9970.020.06799.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALS1.5.0-gbc51d76c-hotfix1data reduction
xia20.5.270-ge1c2909e-dials-1.5data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→47.22 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.261 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 1885 5.1 %RANDOM
Rwork0.1491 ---
obs0.1513 35293 99.91 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.5 Å2 / Biso mean: 28.175 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.26 Å20 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.42→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 19 79 1417
Biso mean--58.15 47.59 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131514
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171613
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.6411967
X-RAY DIFFRACTIONr_angle_other_deg11.1891.6123774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9535.228197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90828.93647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815326
X-RAY DIFFRACTIONr_chiral_restr0.1160.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021661
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02231
X-RAY DIFFRACTIONr_rigid_bond_restr5.67533127
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8580.11
12B8580.11
21A8510.11
22C8510.11
31A7820.15
32D7820.15
41A8530.12
42E8530.12
51A8510.13
52F8510.13
61B8530.1
62C8530.1
71B7760.14
72D7760.14
81B8800.08
82E8800.08
91B8680.1
92F8680.1
101C7790.13
102D7790.13
111C8600.11
112E8600.11
121C8590.11
122F8590.11
131D8130.13
132E8130.13
141D8100.14
142F8100.14
151E7970.11
152F7970.11
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 154 -
Rwork0.358 2548 -
all-2702 -
obs--99.45 %

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