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- PDB-4pnd: A de novo designed pentameric coiled coil CC-Pent_Variant -

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Basic information

Entry
Database: PDB / ID: 4pnd
TitleA de novo designed pentameric coiled coil CC-Pent_Variant
ComponentsCC-Pent_Variant
KeywordsDE NOVO PROTEIN / artificially designed - often synthetic / alpha-helical barrel / coiled coil / protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsWood, C.W. / Burton, A.J. / Thomson, A.R. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council340764 United Kingdom
Engineering and Physical Sciences Research CouncilEP/J001430/3 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J008990/1 United Kingdom
CitationJournal: Science / Year: 2014
Title: Computational design of water-soluble alpha-helical barrels.
Authors: Thomson, A.R. / Wood, C.W. / Burton, A.J. / Bartlett, G.J. / Sessions, R.B. / Brady, R.L. / Woolfson, D.N.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Revision 2.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Pent_Variant
B: CC-Pent_Variant
C: CC-Pent_Variant
D: CC-Pent_Variant
E: CC-Pent_Variant


Theoretical massNumber of molelcules
Total (without water)17,8865
Polymers17,8865
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-89 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.950, 42.560, 97.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
CC-Pent_Variant


Mass: 3577.283 Da / Num. of mol.: 5 / Source method: obtained synthetically
Details: The molecule was synthesised using solid phase peptide synthesis.
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.28 %
Crystal growTemperature: 293.17 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M Ammonium Sulphate, 0.1 M MES, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→48.5 Å / Num. all: 120154 / Num. obs: 14016 / % possible obs: 100 % / Redundancy: 8.6 % / Net I/σ(I): 15.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 9 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.75→48.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 695 4.98 %
Rwork0.1926 --
obs0.1942 13961 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 0 69 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071288
X-RAY DIFFRACTIONf_angle_d0.9191712
X-RAY DIFFRACTIONf_dihedral_angle_d14.278519
X-RAY DIFFRACTIONf_chiral_restr0.048203
X-RAY DIFFRACTIONf_plane_restr0.004209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.88520.31081390.22472602X-RAY DIFFRACTION100
1.8852-2.07490.23261410.20262589X-RAY DIFFRACTION100
2.0749-2.37520.23381540.17862605X-RAY DIFFRACTION100
2.3752-2.99240.20491200.18712675X-RAY DIFFRACTION100
2.9924-48.51860.21641410.19342795X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.8686 Å / Origin y: -2.33 Å / Origin z: -12.047 Å
111213212223313233
T0.0981 Å2-0.0106 Å2-0.0161 Å2-0.1694 Å2-0.0022 Å2--0.0843 Å2
L1.8776 °20.1784 °20.0965 °2-4.6439 °2-0.4012 °2--1.9313 °2
S0.0604 Å °0.0976 Å °0.0004 Å °-0.1604 Å °-0.0057 Å °0.1678 Å °0.0052 Å °-0.0542 Å °-0.0429 Å °
Refinement TLS groupSelection details: all

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