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- PDB-7tml: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

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Basic information

Entry
Database: PDB / ID: 7tml
TitlePorous framework formed by assembly of a bipyridyl-conjugated helical peptide
Componentsbipyridyl-conjugated helical peptide
KeywordsDE NOVO PROTEIN / porous / framework / helix / 310 / alpha / assembly / bipyridine / UIC-1
Function / homologyACETONITRILE / iodobenzene
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsNguyen, A.I.
Funding support1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Assembly of pi-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework.
Authors: Heinz-Kunert, S.L. / Pandya, A. / Dang, V.T. / Tran, P.N. / Ghosh, S. / McElheny, D. / Santarsiero, B.D. / Ren, Z. / Nguyen, A.I.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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_distant_solvent_atoms / 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_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_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_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_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_1 / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6203
Polymers1,3751
Non-polymers2452
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.760, 13.394, 27.732
Angle α, β, γ (deg.)90.000, 97.651, 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: 1374.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PIH / iodobenzene


Mass: 204.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5I
#3: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water acetonitrile and iodobenzene

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 0.711 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.711 Å / Relative weight: 1
ReflectionResolution: 0.93→8.78 Å / Num. obs: 6833 / % possible obs: 98.34 % / Redundancy: 2 % / Biso Wilson estimate: 4.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0736 / Net I/σ(I): 10.7
Reflection shellResolution: 0.93→0.963 Å / Num. unique obs: 683 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
APEXdata reduction
APEXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TLS

7tls


Resolution: 0.93→8.78 Å / SU ML: 0.0894 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 316 4.63 %
Rwork0.1821 6515 -
obs0.1839 6831 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.31 Å2
Refinement stepCycle: LAST / Resolution: 0.93→8.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 29 8 118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092165
X-RAY DIFFRACTIONf_angle_d1.8472223
X-RAY DIFFRACTIONf_chiral_restr0.041110
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d36.390938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.93-1.170.24881470.2183207X-RAY DIFFRACTION97.9
1.17-8.780.20831690.16723308X-RAY DIFFRACTION99.14

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