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- PDB-8gkx: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

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Basic information

Entry
Database: PDB / ID: 8gkx
TitlePorous framework formed by assembly of a bipyridyl-conjugated helical peptide
Componentsbipyridyl-conjugated helical peptide
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 Å
AuthorsHess, S.S. / Nguyen, A.I.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks.
Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / Nguyen, A.I.
History
DepositionMar 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 2.0Sep 25, 2024Group: Advisory / Atomic model ...Advisory / 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 / 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_close_contact / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _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.occupancy / _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_asym_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_alt_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 / _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_close_contact.auth_seq_id_2 / _struct_conf.beg_label_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.entity_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bipyridyl-conjugated helical peptide
B: bipyridyl-conjugated helical peptide


Theoretical massNumber of molelcules
Total (without water)2,8552
Polymers2,8552
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.158, 48.141, 17.967
Angle α, β, γ (deg.)90.000, 93.768, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide bipyridyl-conjugated helical peptide


Mass: 1427.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: Water/Acetonitrile

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.81→17.93 Å / Num. obs: 32406 / % possible obs: 97.34 % / Redundancy: 6.1 % / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.1108 / Net I/σ(I): 11.26
Reflection shellResolution: 0.81→0.839 Å / Rmerge(I) obs: 0.557 / Num. unique obs: 1718

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.81→17.93 Å / SU ML: 0.0809 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1381 3184 9.83 %
Rwork0.1256 29222 -
obs0.1268 32406 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.03 Å2
Refinement stepCycle: LAST / Resolution: 0.81→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms170 0 38 19 227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119222
X-RAY DIFFRACTIONf_angle_d1.9129309
X-RAY DIFFRACTIONf_chiral_restr0.046319
X-RAY DIFFRACTIONf_plane_restr0.012637
X-RAY DIFFRACTIONf_dihedral_angle_d36.701838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.81-0.820.35811650.3451204X-RAY DIFFRACTION88.95
0.82-0.830.28661280.29521243X-RAY DIFFRACTION90.38
0.83-0.850.33531160.27251305X-RAY DIFFRACTION91.27
0.85-0.860.2361210.24781192X-RAY DIFFRACTION91.12
0.86-0.880.25571350.23941204X-RAY DIFFRACTION90.9
0.88-0.90.27961470.22191247X-RAY DIFFRACTION91.53
0.9-0.910.191440.20091286X-RAY DIFFRACTION92.74
0.91-0.930.17621130.16481274X-RAY DIFFRACTION93.09
0.93-0.960.17561340.14911236X-RAY DIFFRACTION94.42
0.96-0.980.16551300.14971259X-RAY DIFFRACTION92.42
0.98-1.010.15031440.12991285X-RAY DIFFRACTION90.16
1.01-1.040.14021350.12211117X-RAY DIFFRACTION86.05
1.04-1.070.11441290.10711305X-RAY DIFFRACTION96.31
1.07-1.110.10281510.09761340X-RAY DIFFRACTION97.71
1.11-1.150.11011470.0941269X-RAY DIFFRACTION96.72
1.15-1.20.09641420.09391343X-RAY DIFFRACTION97.5
1.2-1.270.10051500.09331341X-RAY DIFFRACTION96.44
1.27-1.350.09471370.09691267X-RAY DIFFRACTION97.84
1.35-1.450.12191410.11321375X-RAY DIFFRACTION97.24
1.45-1.60.09581470.10911241X-RAY DIFFRACTION95.86
1.6-1.830.13521270.1131217X-RAY DIFFRACTION88.54
1.83-2.30.10571410.0981340X-RAY DIFFRACTION99
2.3-17.930.13781600.10991332X-RAY DIFFRACTION98.68

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