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

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Basic information

Entry
Database: PDB / ID: 2oxk
TitleHelix Bundle Quaternary Structure from alpha/beta-Peptide Foldamers: GCN4-pLI with beta-residues at b and f heptad positions.
Componentshybrid alpha/beta peptide based on the GCN4-pLI sequence; heptad positions b and f substituted with beta-amino acids
KeywordsUNKNOWN FUNCTION / helix bundle / foldamer
Function / homologyFORMIC ACID
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 22, 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_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4276
Polymers4,1971
Non-polymers2305
Water23413
1
A: hybrid alpha/beta peptide based on the GCN4-pLI sequence; heptad positions b and f substituted with beta-amino acids
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)17,70924
Polymers16,7884
Non-polymers92020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area8750 Å2
ΔGint-74 kcal/mol
Surface area9650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.847, 34.847, 47.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-35-

FMT

21A-39-

HOH

31A-51-

HOH

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Components

#1: Protein/peptide hybrid alpha/beta peptide based on the GCN4-pLI sequence; heptad positions b and f substituted with beta-amino acids


Mass: 4197.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.7 Å3/Da / Density % sol: 27.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.5 M ammonium formate, pH 7.5, 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: Sep 21, 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→47.1 Å / Num. all: 2220 / Num. obs: 2220 / % possible obs: 100 % / Redundancy: 10.9 % / Rsym value: 6.6 / Net I/σ(I): 20.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 42.2 / % possible all: 99.7

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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: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25149 103 4.7 %RANDOM
Rwork0.21244 ---
obs0.21452 2104 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 0 15 13 314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022304
X-RAY DIFFRACTIONr_bond_other_d0.0090.02237
X-RAY DIFFRACTIONr_angle_refined_deg2.3682.223391
X-RAY DIFFRACTIONr_angle_other_deg1.3273579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.396514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1762310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0481556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.913153
X-RAY DIFFRACTIONr_chiral_restr0.120.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0250
X-RAY DIFFRACTIONr_nbd_refined0.1920.242
X-RAY DIFFRACTIONr_nbd_other0.220.2241
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2104
X-RAY DIFFRACTIONr_nbtor_other0.0950.2213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.5178
X-RAY DIFFRACTIONr_mcbond_other0.2331.580
X-RAY DIFFRACTIONr_mcangle_it1.6192270
X-RAY DIFFRACTIONr_scbond_it2.9423126
X-RAY DIFFRACTIONr_scangle_it4.2834.5121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 5 -
Rwork0.287 152 -
obs--99.37 %

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