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- PDB-3f87: An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Co... -

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Basic information

Entry
Database: PDB / ID: 3f87
TitleAn alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quarternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions - higher symmetry crystal
ComponentsGCN4pLI-betaAD
KeywordsUNKNOWN FUNCTION / alpha/beta-peptide / helix bundle / foldamer / GCN4 derivative
Function / homologyIODIDE ION
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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_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_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

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Assembly

Deposited unit
A: GCN4pLI-betaAD
B: GCN4pLI-betaAD
C: GCN4pLI-betaAD
D: GCN4pLI-betaAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,99113
Polymers16,8484
Non-polymers1,1429
Water1,42379
1
A: GCN4pLI-betaAD
B: GCN4pLI-betaAD
hetero molecules

A: GCN4pLI-betaAD
B: GCN4pLI-betaAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,62518
Polymers16,8484
Non-polymers1,77714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
2
C: GCN4pLI-betaAD
D: GCN4pLI-betaAD
hetero molecules

C: GCN4pLI-betaAD
D: GCN4pLI-betaAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3568
Polymers16,8484
Non-polymers5084
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)71.313, 71.313, 97.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains half of two separate, NCS-related tetrameric helix bundles: The second half of the first tetramer, which contains chains A and B, is generated by: (-y, -x, -z+1/2) + (010) / The asymmetric unit contains half of two separate, NCS-related tetrameric helix bundles: The second half of the second tetramer, which contains chains C and D, is generated by: (y, x, -z) + (100)

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Components

#1: Protein/peptide
GCN4pLI-betaAD


Mass: 4212.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic Peptide / References: PDB-3F86
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M NaI, 0.08 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: Jun 21, 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: 2.4→50.4 Å / Num. all: 10451 / Num. obs: 10316 / % possible obs: 98.7 % / Redundancy: 12.61 % / Rmerge(I) obs: 0.148 / Rsym value: 0.061
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.76 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.41 / Num. unique all: 1096 / Rsym value: 0.228 / % possible all: 99.5

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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: 2.4→50.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.794 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 490 4.8 %RANDOM
Rwork0.23 ---
all0.233 9808 --
obs0.233 9808 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 9 79 1264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211221
X-RAY DIFFRACTIONr_bond_other_d0.0260.02972
X-RAY DIFFRACTIONr_angle_refined_deg2.0112.2131609
X-RAY DIFFRACTIONr_angle_other_deg1.39332391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.543557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49125.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.508157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0131077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.013212
X-RAY DIFFRACTIONr_mcbond_it0.671.5682
X-RAY DIFFRACTIONr_mcbond_other1.4781.5313
X-RAY DIFFRACTIONr_mcangle_it1.3621079
X-RAY DIFFRACTIONr_scbond_it2.1813539
X-RAY DIFFRACTIONr_scangle_it3.7854.5525
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 32 -
Rwork0.24 723 -
obs-723 99.47 %

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