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- PDB-8vpt: UIC-14-BPE extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vpt
TitleUIC-14-BPE extension of UIC-1
ComponentsUIC-14-BPE
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsGanatra, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Diverse Proteomimetic Frameworks via Rational Design of pi-Stacking Peptide Tectons.
Authors: Ganatra, P. / Wang, D.F. / Ganatra, V. / Dang, V.T. / Nguyen, A.I.
History
DepositionJan 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UIC-14-BPE
B: UIC-14-BPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6675
Polymers3,5442
Non-polymers1233
Water63135
1
A: UIC-14-BPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8543
Polymers1,7721
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-14-BPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8132
Polymers1,7721
Non-polymers411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)14.050, 16.560, 28.675
Angle α, β, γ (deg.)97.990, 95.020, 90.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide UIC-14-BPE


Mass: 1772.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CCN / ACETONITRILE


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


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: acetonitrile water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.94→16.4 Å / Num. obs: 13900 / % possible obs: 83.79 % / Redundancy: 3.5 % / Biso Wilson estimate: 4.45 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.63
Reflection shellResolution: 0.94→0.9737 Å / Num. unique obs: 1466 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.94→16.4 Å / SU ML: 0.0918 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.5024
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1924 2459 9.98 %
Rwork0.1646 22174 -
obs0.1673 13900 74.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.91 Å2
Refinement stepCycle: LAST / Resolution: 0.94→16.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms218 0 47 35 300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084284
X-RAY DIFFRACTIONf_angle_d1.7233402
X-RAY DIFFRACTIONf_chiral_restr0.048220
X-RAY DIFFRACTIONf_plane_restr0.006646
X-RAY DIFFRACTIONf_dihedral_angle_d32.406575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.960.25261420.25341291X-RAY DIFFRACTION80.24
0.96-0.980.28181560.23231358X-RAY DIFFRACTION81.22
0.98-10.22991430.22341351X-RAY DIFFRACTION79.22
1-1.020.19441420.22561245X-RAY DIFFRACTION77.83
1.02-1.050.23631300.21281273X-RAY DIFFRACTION76.5
1.05-1.080.20011430.20181268X-RAY DIFFRACTION75.45
1.08-1.110.21241380.20041238X-RAY DIFFRACTION75.03
1.11-1.140.18891380.20091222X-RAY DIFFRACTION73.28
1.14-1.180.24331300.17661143X-RAY DIFFRACTION69.41
1.18-1.230.21381200.18311102X-RAY DIFFRACTION66.34
1.23-1.290.18891280.16511164X-RAY DIFFRACTION68.29
1.29-1.360.2161300.16221183X-RAY DIFFRACTION72.78
1.36-1.440.18891320.16691225X-RAY DIFFRACTION73.83
1.44-1.550.15311360.16591232X-RAY DIFFRACTION72.46
1.55-1.710.17981260.1551131X-RAY DIFFRACTION71.02
1.71-1.950.17951410.15321241X-RAY DIFFRACTION73.98
1.95-2.460.20461230.13451075X-RAY DIFFRACTION65.61
2.46-16.40.16351610.12561432X-RAY DIFFRACTION85.65

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