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- PDB-2oxj: Helix Bundle Quaternary Structure from alpha/beta-Peptide Foldame... -

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Basic information

Entry
Database: PDB / ID: 2oxj
TitleHelix Bundle Quaternary Structure from alpha/beta-Peptide Foldamers: GCN4-p1 with beta-residues at b and f heptad positions.
Componentshybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids
KeywordsUNKNOWN FUNCTION / helix bundle / foldamer
Function / homologyACETATE ION
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorne, W.S. / Price, J.L. / Keck, J.L. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Helix Bundle Quaternary Structure from alpha/beta-Peptide Foldamers.
Authors: Horne, W.S. / Price, J.L. / Keck, J.L. / Gellman, S.H.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jul 10, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: hybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids
B: hybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids
C: hybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5274
Polymers12,4683
Non-polymers591
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-42 kcal/mol
Surface area6270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)25.728, 37.641, 92.511
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 hybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids


Mass: 4155.923 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris hydrochloride, 30% w/v PEG 4000, pH 8.5, 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: Aug 31, 2006 / 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→37.6 Å / Num. all: 6503 / Num. obs: 6503 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rsym value: 4.5 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.6 / Rsym value: 29.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.005 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28321 303 4.7 %RANDOM
Rwork0.21875 ---
all0.22178 6169 --
obs0.22178 6169 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.565 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2--0.17 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 4 80 890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022819
X-RAY DIFFRACTIONr_bond_other_d0.0020.02618
X-RAY DIFFRACTIONr_angle_refined_deg2.1582.2191079
X-RAY DIFFRACTIONr_angle_other_deg1.2631524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.852541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79624.58324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51815144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.173155
X-RAY DIFFRACTIONr_chiral_restr0.1090.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02131
X-RAY DIFFRACTIONr_nbd_refined0.2460.2147
X-RAY DIFFRACTIONr_nbd_other0.2250.2638
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2302
X-RAY DIFFRACTIONr_nbtor_other0.0940.2518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.216
X-RAY DIFFRACTIONr_mcbond_it1.2991.5551
X-RAY DIFFRACTIONr_mcbond_other0.2981.5218
X-RAY DIFFRACTIONr_mcangle_it1.7412775
X-RAY DIFFRACTIONr_scbond_it3.2573350
X-RAY DIFFRACTIONr_scangle_it5.1514.5303
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 14 -
Rwork0.275 415 -
obs--97.28 %

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