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- PDB-3f86: An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Co... -

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Basic information

Entry
Database: PDB / ID: 3f86
TitleAn alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quaternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions
ComponentsGCN4pLI-betaAD
KeywordsUNKNOWN FUNCTION / alpha/beta-peptide / helix bundle / foldamer / coiled coil / GCN4 derivative
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGiuliano, M.W. / Horne, W.S. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: An alpha/beta-peptide helix bundle with a pure beta3-amino acid core and a distinctive quaternary structure.
Authors: Giuliano, M.W. / Horne, W.S. / Gellman, S.H.
History
DepositionNov 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq / struct_site
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_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4pLI-betaAD
B: GCN4pLI-betaAD
C: GCN4pLI-betaAD
D: GCN4pLI-betaAD
E: GCN4pLI-betaAD
F: GCN4pLI-betaAD
G: GCN4pLI-betaAD
H: GCN4pLI-betaAD


Theoretical massNumber of molelcules
Total (without water)33,6978
Polymers33,6978
Non-polymers00
Water2,306128
1
A: GCN4pLI-betaAD
B: GCN4pLI-betaAD
C: GCN4pLI-betaAD
D: GCN4pLI-betaAD


Theoretical massNumber of molelcules
Total (without water)16,8484
Polymers16,8484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: GCN4pLI-betaAD
F: GCN4pLI-betaAD
G: GCN4pLI-betaAD
H: GCN4pLI-betaAD


Theoretical massNumber of molelcules
Total (without water)16,8484
Polymers16,8484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.381, 68.720, 48.297
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit of the structure contains two helix bundle tetramers ('biological' units): The first tetramer is composed of chains A, B, C, and D. / The asymmetric unit of the structure contains two helix bundle tetramers ('biological' units): The second tetramer is composed of chains E, F, G, and H.

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Components

#1: Protein/peptide
GCN4pLI-betaAD


Mass: 4212.099 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Synthetic Peptide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaCl, 0.1 M HEPES-Na pH 7.5, 20% (v/v) 2-methyl-2,4-pentanediol (MPD) , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 28, 2007 / Details: confocal mirrors
RadiationMonochromator: Gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→47.4 Å / Num. all: 16772 / Num. obs: 16551 / % possible obs: 98.7 % / Redundancy: 5.91 % / Rmerge(I) obs: 0.055 / Rsym value: 0.0352
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2119 / Rsym value: 0.267 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 842 5.1 %RANDOM
Rwork0.2 ---
all0.203 15753 --
obs0.203 15753 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.11 Å2
2--0.11 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 0 0 128 4931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212296
X-RAY DIFFRACTIONr_bond_other_d0.0010.021776
X-RAY DIFFRACTIONr_angle_refined_deg1.8812.2193018
X-RAY DIFFRACTIONr_angle_other_deg2.95834395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4475105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91826.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.636157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0131972
X-RAY DIFFRACTIONr_gen_planes_other0.0290.012359
X-RAY DIFFRACTIONr_mcbond_it0.71.51327
X-RAY DIFFRACTIONr_mcbond_other3.3711.5614
X-RAY DIFFRACTIONr_mcangle_it1.37422087
X-RAY DIFFRACTIONr_scbond_it2.2293968
X-RAY DIFFRACTIONr_scangle_it3.8164.5927
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 53 -
Rwork0.26 1080 -
obs-1080 92.49 %

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