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- PDB-7baw: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -

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Basic information

Entry
Database: PDB / ID: 7baw
TitleA heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(GgIaId)4
ComponentsCC-Type2-(GgIaId)4
KeywordsDE NOVO PROTEIN / alpha-helical / barrel
Function / homologyN-PROPANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.71 Å
AuthorsMartin, F.J.O. / Dawson, W.M. / 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
Revision 1.2Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification ..._diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,71513
Polymers22,2597
Non-polymers4576
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-113 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.456, 50.434, 126.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA1 - 302 - 31
21GLYGLYBB1 - 302 - 31
12ILEILEAA1 - 282 - 29
22ILEILECC1 - 282 - 29
13GLYGLYAA1 - 302 - 31
23GLYGLYDD1 - 302 - 31
14GLYGLYAA1 - 302 - 31
24GLYGLYEE1 - 302 - 31
15GLYGLYAA1 - 302 - 31
25GLYGLYFF1 - 302 - 31
16ILEILEAA1 - 282 - 29
26ILEILEGG1 - 282 - 29
17ILEILEBB1 - 282 - 29
27ILEILECC1 - 282 - 29
18GLYGLYBB1 - 302 - 31
28GLYGLYDD1 - 302 - 31
19GLYGLYBB1 - 302 - 31
29GLYGLYEE1 - 302 - 31
110GLYGLYBB1 - 302 - 31
210GLYGLYFF1 - 302 - 31
111ILEILEBB1 - 282 - 29
211ILEILEGG1 - 282 - 29
112ILEILECC1 - 282 - 29
212ILEILEDD1 - 282 - 29
113ILEILECC1 - 282 - 29
213ILEILEEE1 - 282 - 29
114ILEILECC1 - 282 - 29
214ILEILEFF1 - 282 - 29
115LYSLYSCC1 - 292 - 30
215LYSLYSGG1 - 292 - 30
116GLYGLYDD1 - 302 - 31
216GLYGLYEE1 - 302 - 31
117GLYGLYDD1 - 302 - 31
217GLYGLYFF1 - 302 - 31
118ILEILEDD1 - 282 - 29
218ILEILEGG1 - 282 - 29
119GLYGLYEE1 - 302 - 31
219GLYGLYFF1 - 302 - 31
120ILEILEEE1 - 282 - 29
220ILEILEGG1 - 282 - 29
121ILEILEFF1 - 282 - 29
221ILEILEGG1 - 282 - 29

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

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


Mass: 3179.818 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 25 mM imidazole, 25 mM MES monohydrate (acid) buffer, 15 mM sodium nitrate, 15 mM sodium phosphate dibasic, 15 mM ammonium sulfate, 10% v/v ethylene glycol, and 5 % w/v PEG 8000 at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50.48 Å / Num. obs: 27241 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 1.78
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 13 % / Rmerge(I) obs: 3.121 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1400 / CC1/2: 0.511 / Rpim(I) all: 0.887 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
ACORNFRAGONphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.71→50.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.845 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1362 5.1 %RANDOM
Rwork0.2333 ---
obs0.2345 25375 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 40.228 Å2 / Biso min: 24.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å2-0 Å2
2--0.04 Å2-0 Å2
3----3 Å2
Refinement stepCycle: final / Resolution: 1.71→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 30 15 1518
Biso mean--72.89 53.69 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181605
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.6311981
X-RAY DIFFRACTIONr_angle_other_deg1.5351.5983698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3635201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64624.12540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69415296
X-RAY DIFFRACTIONr_chiral_restr0.0840.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7860.04
12B7860.04
21A6980.08
22C6980.08
31A7790.09
32D7790.09
41A7840.08
42E7840.08
51A7840.05
52F7840.05
61A7210.08
62G7210.08
71B7070.1
72C7070.1
81B7800.08
82D7800.08
91B7780.09
92E7780.09
101B7820.07
102F7820.07
111B7320.07
112G7320.07
121C7120.11
122D7120.11
131C7000.08
132E7000.08
141C7120.09
142F7120.09
151C7360.12
152G7360.12
161D7700.11
162E7700.11
171D7860.1
172F7860.1
181D7400.08
182G7400.08
191E7870.09
192F7870.09
201E7190.12
202G7190.12
211F7380.11
212G7380.11
LS refinement shellResolution: 1.71→1.754 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 105 -
Rwork0.376 1804 -
all-1909 -
obs--99.69 %
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)
11.1761-0.11090.59271.4516-1.73567.24830.04280.0177-0.03450.00760.0148-0.09270.10580.329-0.05760.0137-0.0025-0.00370.0423-0.01570.093410.739436.440622.3957
21.46560.1823-0.96981.2281-1.35238.5520.0413-0.0253-0.1069-0.02120.0157-0.03510.24360.1607-0.0570.03820.0083-0.02140.0052-0.00420.09296.151429.870922.5976
31.3904-0.0713-0.40361.58622.03499.68890.0493-0.0043-0.01690.0074-0.0060.10270.0435-0.3934-0.04330.01710.0005-0.01050.03320.01880.0909-7.255734.45721.9431
41.9366-0.1181-1.79281.20960.30279.41740.0155-0.0023-0.1077-0.00520.01110.09820.1528-0.1495-0.02660.0284-0.012-0.01890.00620.01030.0907-1.980928.99122.4612
51.5531-0.39261.53691.2481-0.9747.9454-0.04020.0330.04270.02060.0093-0.1006-0.19920.19640.03090.0272-0.02920.00410.033-0.01490.08848.163344.535421.9893
61.90980.09521.62450.7520.37126.1853-0.04030.03260.144-0.01530.0117-0.0147-0.33560.10530.02860.0711-0.00480.0070.004-0.01160.08670.652347.46822.2725
71.57530.43631.2171.37792.00868.0148-0.0153-0.04410.0556-0.0157-0.01060.0953-0.1947-0.36020.02590.04080.029-0.0010.03240.01020.0915-6.906342.824221.8038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 30
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 29
4X-RAY DIFFRACTION4D0 - 30
5X-RAY DIFFRACTION5E0 - 30
6X-RAY DIFFRACTION6F0 - 30
7X-RAY DIFFRACTION7G0 - 29

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