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- PDB-6y13: Bicyclic stapled peptide bp70 at 1.1 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6y13
TitleBicyclic stapled peptide bp70 at 1.1 Angstrom resolution
Componentsbp70
KeywordsANTIBIOTIC / Antimicrobial / Bicyclic / Lectin
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.112 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#1: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#2: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#3: Journal: Chemrxiv / Year: 2021
Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L.
History
DepositionFeb 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.2Feb 2, 2022Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low
Revision 2.0Feb 1, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_rmsd_angle / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_site / struct_site_gen
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.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bp70


Theoretical massNumber of molelcules
Total (without water)1,5341
Polymers1,5341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint1 kcal/mol
Surface area1420 Å2
Unit cell
Length a, b, c (Å)26.856, 26.856, 26.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein/peptide bp70


Mass: 1533.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bicyclic stapled peptide bp70 / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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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: 1.44 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M AMMONIUM SULFATE, 0.1 M MES MONOHYDRATE PH 6.5, 10% V/V 1,4-DIOXANE, 2% V/V GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 20, 2017
Details: COLLIMATING MIRROR (M1), BARTELS MONOCHROMATOR (DCCM), TOROIDAL MIRROR (M2)
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.112→26.16 Å / Num. obs: 7887 / % possible obs: 94.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.083 Å2 / CC1/2: 0.977 / CC star: 0.994 / R split: 0.136 / Rmerge(I) obs: 0.354 / Rpim(I) all: 0.096 / Rrim(I) all: 0.367 / Χ2: 0.83 / Net I/av σ(I): 1.24 / Net I/σ(I): 2.67
Reflection shellResolution: 1.112→1.117 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 897 / CC1/2: 0.163 / Rrim(I) all: 1.24 / % possible all: 67.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.18 Å26.16 Å
Translation2.18 Å26.16 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
SHELXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XXXX

Resolution: 1.112→26.16 Å / Num. parameters: 946 / Num. restraintsaints: 1190 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1278 --RANDOM
Rwork0.1264 ---
all-4332 --
obs-4332 95.58 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 77.47 Å2 / Biso mean: 23.1498 Å2 / Biso min: 6.86 Å2
Refinement stepCycle: final / Resolution: 1.112→26.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms105 0 0 0 105
Num. residues----13
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.049
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.319
X-RAY DIFFRACTIONs_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0

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