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- PDB-7tm2: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

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Basic information

Entry
Database: PDB / ID: 7tm2
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 / homologytert-butylbenzene
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 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: 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 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / 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_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _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)1,7774
Polymers1,3751
Non-polymers4033
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.721, 13.683, 27.803
Angle α, β, γ (deg.)90.000, 96.879, 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-I7E / tert-butylbenzene


Mass: 134.218 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water and 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: 0.619 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.619 Å / Relative weight: 1
ReflectionResolution: 0.88→12.84 Å / Num. obs: 14928 / % possible obs: 95.71 % / Redundancy: 12.4 % / Biso Wilson estimate: 4.54 Å2 / Rmerge(I) obs: 0.06869 / Net I/σ(I): 16.04
Reflection shellResolution: 0.88→0.9114 Å / Rmerge(I) obs: 0.06869 / Num. unique obs: 456

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Processing

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

7tls


Resolution: 0.88→12.84 Å / SU ML: 0.0751 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.1999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1054 1492 9.99 %
Rwork0.0988 13436 -
obs0.0995 14928 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.67 Å2
Refinement stepCycle: LAST / Resolution: 0.88→12.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 49 1 131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133149
X-RAY DIFFRACTIONf_angle_d2.1343209
X-RAY DIFFRACTIONf_chiral_restr0.058410
X-RAY DIFFRACTIONf_plane_restr0.012521
X-RAY DIFFRACTIONf_dihedral_angle_d32.570335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.88-0.910.27721040.2481955X-RAY DIFFRACTION72.09
0.91-0.940.20421240.20921134X-RAY DIFFRACTION89.22
0.94-0.980.17971400.14921299X-RAY DIFFRACTION97.3
0.98-1.020.13371420.13811250X-RAY DIFFRACTION96.4
1.02-1.080.16561470.12021251X-RAY DIFFRACTION96.88
1.08-1.140.11171430.09741291X-RAY DIFFRACTION96.24
1.14-1.230.09021330.08641203X-RAY DIFFRACTION94.89
1.23-1.360.10731340.09131249X-RAY DIFFRACTION95.18
1.36-1.550.11031470.09261277X-RAY DIFFRACTION98.41
1.55-1.950.07831460.08511284X-RAY DIFFRACTION97.74
1.96-12.840.07171320.07381243X-RAY DIFFRACTION96.49

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