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- PDB-7bas: A de novo pentameric coiled-coil assembly: CC-Type2-(TgLaId)4-W19... -

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Basic information

Entry
Database: PDB / ID: 7bas
TitleA de novo pentameric coiled-coil assembly: CC-Type2-(TgLaId)4-W19BrPhe.
ComponentsCC-Type2-(TgLaId)4-W19BrPhe.
KeywordsDE NOVO PROTEIN / alpha / helical / barrel / pentamer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsMartin, F.J.O. / Dawson, W.M. / Shelley, K. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)340764 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB R00661X 1 United Kingdom
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
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 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 / _citation_author.name / _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

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(TgLaId)4-W19BrPhe.
B: CC-Type2-(TgLaId)4-W19BrPhe.
C: CC-Type2-(TgLaId)4-W19BrPhe.
D: CC-Type2-(TgLaId)4-W19BrPhe.
E: CC-Type2-(TgLaId)4-W19BrPhe.


Theoretical massNumber of molelcules
Total (without water)16,9745
Polymers16,9745
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-80 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.560, 54.647, 57.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

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
1050B1 - 30
2050C1 - 30
1060B1 - 30
2060D1 - 30
1070B1 - 30
2070E1 - 30
1080C1 - 30
2080D1 - 30
1090C1 - 30
2090E1 - 30
10100D1 - 30
20100E1 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein/peptide
CC-Type2-(TgLaId)4-W19BrPhe.


Mass: 3394.835 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.6 mM peptide, 50 mM MES, 5 % w/v PEG 5000 MME, 6 % v/v 1-propanol.
Temp details: 20 degC incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.1→57.69 Å / Num. obs: 53567 / % possible obs: 99.2 % / Redundancy: 19.6 % / CC1/2: 0.553 / Rmerge(I) obs: 0.669 / Rpim(I) all: 0.204 / Rrim(I) all: 0.707 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
1.29-1.311416690.26917.33544.33295.6
7.07-57.6916.12720.9990.0260.09799.90.093

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→39.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.669 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 2893 5.1 %RANDOM
Rwork0.181 ---
obs0.1826 53567 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.07 Å2 / Biso mean: 13.836 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-0 Å2
2---0.16 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: final / Resolution: 1.1→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 0 185 1323
Biso mean---23.56 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131159
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171261
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6551521
X-RAY DIFFRACTIONr_angle_other_deg11.1421.5962919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7095139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47229.19431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29915255
X-RAY DIFFRACTIONr_chiral_restr0.070.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02157
X-RAY DIFFRACTIONr_rigid_bond_restr8.08732420
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8340.09
12B8340.09
21A8120.11
22C8120.11
31A8240.09
32D8240.09
41A8290.1
42E8290.1
51B8180.1
52C8180.1
61B8120.1
62D8120.1
71B8220.09
72E8220.09
81C8140.1
82D8140.1
91C8020.12
92E8020.12
101D8130.12
102E8130.12
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0
Num. reflection% reflection
Rfree217 -
Rwork3921 -
obs-99.98 %
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)
110.89050.61531.19951.0289-0.10871.01330.046-0.1261-0.19860.0272-0.0033-0.00620.0725-0.0037-0.04270.00720-0.00070.0022-0.00030.013535.40853.813444.7341
214.9751-1.7251-3.24150.92150.56161.46690.17580.41990.2323-0.172-0.0980.0721-0.1126-0.1319-0.07780.03560.0166-0.0150.0168-0.00020.02933.652714.864535.3957
37.29682.1011-0.75251.701-0.54060.96810.0738-0.11610.19470.0256-0.02550.0613-0.0847-0.0259-0.04830.00850.00360.00060.0072-0.01260.037633.326318.213544.0038
49.56261.49370.50861.5634-0.09671.56980.0987-0.35360.16830.1138-0.09180.0113-0.0170.0111-0.00690.0093-0.0037-0.0010.0231-0.01150.007434.682111.467549.72
514.9085-1.11711.24930.7301-0.22140.80370.05180.3211-0.2553-0.1136-0.08280.02490.11480.01580.0310.03170.00520.00140.02030.00180.021334.9596.078836.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2B0 - 31
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E1 - 31

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