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- PDB-4pnb: A de novo designed hexameric coiled coil CC-Hex3. -

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Open data


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Basic information

Entry
Database: PDB / ID: 4pnb
TitleA de novo designed hexameric coiled coil CC-Hex3.
ComponentsCC-Hex3
KeywordsDE NOVO PROTEIN / Artificially designed - often synthetic / Alpha-helical barrel / coiled coil / protein design / peptide .
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 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 / Author supporting evidence
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / 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.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _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
Revision 2.2Oct 9, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 2.3Dec 11, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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-Hex3
B: CC-Hex3
C: CC-Hex3
D: CC-Hex3


Theoretical massNumber of molelcules
Total (without water)13,2034
Polymers13,2034
Non-polymers00
Water1,33374
1
A: CC-Hex3

A: CC-Hex3

A: CC-Hex3

B: CC-Hex3

B: CC-Hex3

B: CC-Hex3


Theoretical massNumber of molelcules
Total (without water)19,8056
Polymers19,8056
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation16_555x,-y,-z+1/21
crystal symmetry operation20_555-z+1/2,x,-y1
crystal symmetry operation24_555-y,-z+1/2,x1
Buried area8440 Å2
ΔGint-88 kcal/mol
Surface area10400 Å2
MethodPISA
2
C: CC-Hex3
D: CC-Hex3

C: CC-Hex3
D: CC-Hex3

C: CC-Hex3
D: CC-Hex3


Theoretical massNumber of molelcules
Total (without water)19,8056
Polymers19,8056
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area7920 Å2
ΔGint-85 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.210, 89.210, 89.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

21A-119-

HOH

31A-120-

HOH

41A-121-

HOH

51B-102-

HOH

61C-113-

HOH

71C-114-

HOH

81C-115-

HOH

91C-116-

HOH

101D-114-

HOH

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Components

#1: Protein/peptide
CC-Hex3


Mass: 3300.863 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 10 % w/v PEG 2000 MME.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→44.61 Å / Num. obs: 7572 / % possible obs: 100 % / Redundancy: 13.7 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 13 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.052→44.6 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 348 4.61 %
Rwork0.2411 --
obs0.2428 7557 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 0 74 975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008928
X-RAY DIFFRACTIONf_angle_d1.0951219
X-RAY DIFFRACTIONf_dihedral_angle_d15.362355
X-RAY DIFFRACTIONf_chiral_restr0.09144
X-RAY DIFFRACTIONf_plane_restr0.003143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.052-2.58530.32091600.23353567X-RAY DIFFRACTION100
2.5853-44.61550.26211880.2443642X-RAY DIFFRACTION100

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