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- PDB-8vxs: UIC-15-BPE extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vxs
TitleUIC-15-BPE extension of UIC-1
ComponentsUIC-15-BPE extension of UIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
DepositionFeb 6, 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
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-15-BPE extension of UIC-1
B: UIC-15-BPE extension of UIC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8927
Polymers3,6862
Non-polymers2055
Water28816
1
A: UIC-15-BPE extension of UIC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9664
Polymers1,8431
Non-polymers1233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-15-BPE extension of UIC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9253
Polymers1,8431
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.240, 14.070, 36.500
Angle α, β, γ (deg.)90.000, 120.860, 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 UIC-15-BPE extension of UIC-1


Mass: 1843.137 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.: 5 / Source method: obtained synthetically / Formula: C2H3N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 1.2→28.31 Å / Num. obs: 7727 / % possible obs: 89.99 % / Redundancy: 11.8 % / Biso Wilson estimate: 9.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.66
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 727 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→28.31 Å / SU ML: 0.1039 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1758 1455 10.1 %
Rwork0.1323 12957 -
obs0.1368 7727 89.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.61 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms228 0 53 16 297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082280
X-RAY DIFFRACTIONf_angle_d1.8836392
X-RAY DIFFRACTIONf_chiral_restr0.047222
X-RAY DIFFRACTIONf_plane_restr0.005944
X-RAY DIFFRACTIONf_dihedral_angle_d34.926256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.24411380.19221226X-RAY DIFFRACTION83.37
1.24-1.290.25721460.17561295X-RAY DIFFRACTION89.17
1.29-1.350.19311480.15771308X-RAY DIFFRACTION90.32
1.35-1.420.20711460.15811277X-RAY DIFFRACTION88.61
1.42-1.510.21161300.13991218X-RAY DIFFRACTION83.94
1.51-1.630.16421470.13641341X-RAY DIFFRACTION92.08
1.63-1.790.17631510.12631361X-RAY DIFFRACTION93.33
1.79-2.050.19631430.12191253X-RAY DIFFRACTION86.71
2.05-2.580.11681540.11511325X-RAY DIFFRACTION92.9
2.59-28.310.17781520.12541353X-RAY DIFFRACTION93.42

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