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- PDB-7tm1: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

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Basic information

Entry
Database: PDB / ID: 7tm1
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
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsNguyen, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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_symm_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_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.label_alt_id_1 / _pdbx_validate_symm_contact.label_alt_id_2 / _pdbx_validate_symm_contact.site_symmetry_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_symmetry / _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
C: bipyridyl-conjugated helical peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3454
Polymers4,3043
Non-polymers411
Water905
1
A: bipyridyl-conjugated helical peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4762
Polymers1,4351
Non-polymers411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: bipyridyl-conjugated helical peptide


Theoretical massNumber of molelcules
Total (without water)1,4351
Polymers1,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: bipyridyl-conjugated helical peptide


Theoretical massNumber of molelcules
Total (without water)1,4351
Polymers1,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.749, 11.566, 27.904
Angle α, β, γ (deg.)90.000, 107.416, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide bipyridyl-conjugated helical peptide


Mass: 1434.707 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CCN / ACETONITRILE


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
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: 0.976 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.1→26.62 Å / Num. obs: 17817 / % possible obs: 95.64 % / Redundancy: 3.9 % / Biso Wilson estimate: 6.94 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.228 / Net I/σ(I): 9.55
Reflection shellResolution: 1.1→1.139 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 849 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: energy minimized helix

Resolution: 1.1→26.62 Å / SU ML: 0.0898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1628 1749 9.82 %
Rwork0.1448 16068 -
obs0.1467 17817 93.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.75 Å2
Refinement stepCycle: LAST / Resolution: 1.1→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms252 0 60 5 317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124383
X-RAY DIFFRACTIONf_angle_d2.2411530
X-RAY DIFFRACTIONf_chiral_restr0.045125
X-RAY DIFFRACTIONf_plane_restr0.013262
X-RAY DIFFRACTIONf_dihedral_angle_d43.174268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.23541110.21961150X-RAY DIFFRACTION77.98
1.13-1.170.25361440.19571371X-RAY DIFFRACTION92.21
1.17-1.210.21351400.20491365X-RAY DIFFRACTION97.66
1.21-1.260.25531600.19411375X-RAY DIFFRACTION96.12
1.26-1.320.22791500.19511373X-RAY DIFFRACTION95.67
1.32-1.390.18651360.18391353X-RAY DIFFRACTION93.94
1.39-1.470.20971530.15361299X-RAY DIFFRACTION91.49
1.47-1.590.15891510.13641395X-RAY DIFFRACTION96.81
1.59-1.750.15811550.12971343X-RAY DIFFRACTION95.84
1.75-20.15291620.13431386X-RAY DIFFRACTION95.91
2-2.520.14811450.11651282X-RAY DIFFRACTION90.32
2.52-26.620.10121420.11621376X-RAY DIFFRACTION95.41

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