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- PDB-8a3k: X-ray crystal structure of a de novo designed single-chain antipa... -

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Basic information

Entry
Database: PDB / ID: 8a3k
TitleX-ray crystal structure of a de novo designed single-chain antiparallel 4-helix coiled-coil bundle, sc-apCC-4
Componentssc-apCC-4
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / de novo protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlbanese, K.I. / Mylemans, B. / Naudin, E.A. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V004220/1 United Kingdom
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Chem Sci / Year: 2022
Title: From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.
Authors: Naudin, E.A. / Albanese, K.I. / Smith, A.J. / Mylemans, B. / Baker, E.G. / Weiner, O.D. / Andrews, D.M. / Tigue, N. / Savery, N.J. / Woolfson, D.N.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
UNK: sc-apCC-4


Theoretical massNumber of molelcules
Total (without water)15,2891
Polymers15,2891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.082, 38.856, 56.828
Angle α, β, γ (deg.)90.000, 101.884, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein sc-apCC-4


Mass: 15288.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2- propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.2 M 1,3-propanediol, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9253 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 2→31.85 Å / Num. obs: 7661 / % possible obs: 93 % / Redundancy: 2.4 % / Biso Wilson estimate: 47.31 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.024 / Χ2: 0.68 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 547 / CC1/2: 0.663 / Rpim(I) all: 0.673 / Χ2: 1.11 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apCC-Tet*

Resolution: 2→31.85 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.0321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276 345 4.51 %
Rwork0.2364 7306 -
obs0.2385 7651 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.19 Å2
Refinement stepCycle: LAST / Resolution: 2→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 0 0 823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056828
X-RAY DIFFRACTIONf_angle_d0.83021132
X-RAY DIFFRACTIONf_chiral_restr0.041152
X-RAY DIFFRACTIONf_plane_restr0.006141
X-RAY DIFFRACTIONf_dihedral_angle_d14.3283255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.520.29081460.27223696X-RAY DIFFRACTION94.14
2.52-31.850.27361990.22923610X-RAY DIFFRACTION91.61
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)
13.97564632084-1.733491425211.156395434115.96956408611-2.458478491834.2715291418-0.112608775664-0.192763854565-0.02808932798040.5523135555860.0274035120048-0.232229804084-0.0933505519690.08661413873570.07905865703050.422934302258-0.0496555501764-0.1520991918680.237747882727-0.01146639747510.5678031185193.94174509904-2.57929035847-14.6622690393
21.107127882381.90440795664-0.9145220327453.28328928771-1.540380750051.602694240540.04562287100510.191193452031.068654174890.0521111620476-0.265165533791.21981872031-0.865202270809-1.046781769950.179440648330.6837441902960.191081970958-0.1142061093570.3753804678990.1031315618170.95334655454-2.9113379497212.9354936287-29.9904102929
32.722866851130.2478475429721.114631505377.233871139854.877023554573.617262689240.278177754258-0.0161379452135-0.1890196759230.6289703944880.525148623912-0.9280567514441.239913782430.878221757144-0.6545228251370.957679522369-0.16981507975-0.4213792249750.6474035288270.1725955280041.2253287849517.4776656778-18.0583133446-4.12345185152
40.191488565185-0.802072764511.369335074483.34040299681-5.705597825689.74261563393-0.22028764648-0.3425196573420.213870959481-0.143224392392-0.2510051878650.487192826617-1.52354386181-0.6392168085480.4017381129661.144868710130.147346650037-0.09315099520420.859494347835-0.242218657711.23741693505-8.3959648796815.229099027-21.6180914003
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: UNK / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'C' and (resid 0 through 29 or resid 37 through 63 or resid 70 through 97 or resid 104 through 130 )0 - 1301 - 127
22chain 'C' and (resid 30 through 36 )30 - 3631 - 37
33chain 'C' and (resid 66 through 69 )66 - 6965 - 68
44chain 'C' and (resid 100 through 103 )100 - 10397 - 100

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