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- PDB-4pn9: A de novo designed hexameric coiled coil CC-Hex2 -

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Basic information

Entry
Database: PDB / ID: 4pn9
TitleA de novo designed hexameric coiled coil CC-Hex2
ComponentsCC-Hex2
KeywordsDE NOVO PROTEIN / alpha-helical barrel / coiled coil / protein design
Biological speciesSynthetic Construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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/J001430/1 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 ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / struct_site_gen
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 / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _struct_site_gen.auth_seq_id
Revision 2.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hex2
B: CC-Hex2
C: CC-Hex2
D: CC-Hex2
E: CC-Hex2
F: CC-Hex2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0567
Polymers19,8186
Non-polymers2381
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-77 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.320, 125.530, 58.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide
CC-Hex2


Mass: 3302.965 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Synthetic Construct (others)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Na HEPES, 4.3 M Sodium Chloride

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→42.66 Å / Num. all: 33093 / Num. obs: 11120 / % possible obs: 98.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3 % / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: search model was in silico

Resolution: 2.2→42.657 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 530 4.78 %
Rwork0.2063 --
obs0.2088 11080 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 15 68 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071406
X-RAY DIFFRACTIONf_angle_d1.0981853
X-RAY DIFFRACTIONf_dihedral_angle_d14.205566
X-RAY DIFFRACTIONf_chiral_restr0.039216
X-RAY DIFFRACTIONf_plane_restr0.006203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.42150.30571270.25572606X-RAY DIFFRACTION97
2.4215-2.77180.27361250.22282620X-RAY DIFFRACTION98
2.7718-3.49190.26171370.21112619X-RAY DIFFRACTION97
3.4919-42.66450.23511410.18382705X-RAY DIFFRACTION97
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)
13.8320.1877-0.99072.3698-0.85824.2971-0.0339-0.0763-0.24590.2581-0.08740.56740.2938-0.26730.09670.2351-0.07760.01860.2919-0.02430.287768.9734273.242261.1349
22.4458-0.2469-0.5612.45120.35554.8116-0.0194-0.4034-0.20430.9982-0.24590.04270.29340.10370.30430.2906-0.08030.02170.39370.02430.275774.1408271.96868.6748
34.2957-1.6502-0.99858.30712.40064.80080.0765-1.0286-0.11160.8180.0303-0.71630.58040.751-0.25750.281-0.0151-0.03640.5790.17480.32182.8871272.263467.9966
42.683-0.8298-1.71223.08120.86054.1998-0.1004-0.5413-0.2489-0.27870.1933-0.44580.20741.0663-0.12530.2570.14030.00680.5580.11710.326187.0013272.823460.0557
53.9151.7078-0.41368.2816-0.10153.8447-0.0486-0.0778-0.1222-0.6558-0.3253-0.07840.44150.79560.23650.32330.18580.04280.45650.06980.265782.0914273.724652.6941
62.80360.7070.18722.5173-0.20034.31480.09890.15320.0045-0.1589-0.20920.62030.3296-0.00920.04680.24040.0646-0.03570.3686-0.05660.302373.0815273.988153.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 29 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 30 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 30 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 30 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 30 )

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