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

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Basic information

Entry
Database: PDB / ID: 7bav
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 / AB INITIO PHASING / Resolution: 1.3 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
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-78 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.734, 51.831, 55.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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.: 122 / 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: 1.84 Å3/Da / Density % sol: 33.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 600 mM peptide, 50 mM potassium chloride, 50 mM Na HEPES, 7.5 % w/v PEG 5000 MME
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: 1.3→43.73 Å / Num. obs: 31472 / % possible obs: 99.9 % / Redundancy: 17.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.043 / Rrim(I) all: 0.178 / Net I/σ(I): 7.4 / Num. measured all: 540575 / Scaling rejects: 947
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3214.75.0722197714980.4461.3585.2550.897.1
7.12-43.7314.60.0635522430.9980.0170.06321.199.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
ACORNFragonphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.3→37.76 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.842 / SU ML: 0.053 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1531 4.9 %RANDOM
Rwork0.1859 ---
obs0.1874 29873 99.93 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 146.97 Å2 / Biso mean: 22.517 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-0 Å2
2--1.28 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.3→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 0 122 1268
Biso mean---30.87 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131169
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171281
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6611537
X-RAY DIFFRACTIONr_angle_other_deg11.0471.62973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7925143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1327.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76715260
X-RAY DIFFRACTIONr_chiral_restr0.1010.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021146
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02162
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8300.13
12B8300.13
21A8410.11
22C8410.11
31A8430.12
32D8430.12
41A8360.11
42E8360.11
51B8220.12
52C8220.12
61B8160.13
62D8160.13
71B8160.1
72E8160.1
81C8330.12
82D8330.12
91C8330.1
92E8330.1
101D8390.12
102E8390.12
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 111 -
Rwork0.375 2145 -
all-2256 -
obs--99.08 %
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)
116.398-0.8714.41151.4315-0.29922.89660.250.0229-0.4049-0.0068-0.11570.00810.2933-0.0745-0.13430.0437-0.0140.00590.0209-0.00520.036820.275519.287118.9465
214.60381.98971.88931.04630.13881.41590.06-0.4122-0.19730.1355-0.06050.0309-0.0153-0.0150.00060.0222-0.00220.00320.0130.0050.035519.047724.04226.4452
315.4925-2.72850.01392.0052-0.05261.30950.13330.15190.4754-0.1434-0.0759-0.136-0.17410.0513-0.05730.0355-0.00080.0140.00590.00140.026920.642933.654115.4775
49.9934-2.12142.34171.5371-0.4671.82580.15350.2875-0.0767-0.1803-0.1075-0.00360.07580.0401-0.0460.02490.00810.00560.014-0.010.027821.109625.034212.0574
514.92961.4773-0.31471.2015-0.30261.47450.0721-0.27870.2370.1279-0.0254-0.0126-0.17780.0474-0.04670.0321-0.009-0.00630.01090.00470.03319.823932.627124.3628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 30
2X-RAY DIFFRACTION2B1 - 31
3X-RAY DIFFRACTION3C0 - 31
4X-RAY DIFFRACTION4D0 - 30
5X-RAY DIFFRACTION5E1 - 30

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