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- PDB-8vps: UIC-12-BPE extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vps
TitleUIC-12-BPE extension of UIC-1
ComponentsUIC-12-BPE
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyDIMETHYLFORMAMIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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-12-BPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6892
Polymers1,6161
Non-polymers731
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.308, 9.960, 19.974
Angle α, β, γ (deg.)90.000, 94.020, 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
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: Protein/peptide UIC-12-BPE


Mass: 1615.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: DMF, water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.729317 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729317 Å / Relative weight: 1
ReflectionResolution: 1→19.92 Å / Num. obs: 5614 / % possible obs: 98.11 % / Redundancy: 6.5 % / Biso Wilson estimate: 9.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 1→1.036 Å / Num. unique obs: 525 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→19.92 Å / SU ML: 0.0831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1462 1039 10 %
Rwork0.1281 9348 -
obs0.1302 5614 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.45 Å2
Refinement stepCycle: LAST / Resolution: 1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 24 9 131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102131
X-RAY DIFFRACTIONf_angle_d1.8458187
X-RAY DIFFRACTIONf_chiral_restr0.058411
X-RAY DIFFRACTIONf_plane_restr0.008422
X-RAY DIFFRACTIONf_dihedral_angle_d34.591527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.050.21561600.22491337X-RAY DIFFRACTION99.6
1.05-1.120.20211340.16911291X-RAY DIFFRACTION93.38
1.12-1.20.15961440.15911333X-RAY DIFFRACTION99.33
1.21-1.330.16081510.14271322X-RAY DIFFRACTION96.4
1.33-1.520.17371500.14851354X-RAY DIFFRACTION97.85
1.52-1.910.13381600.1311337X-RAY DIFFRACTION98.68
1.91-19.920.12631400.10491374X-RAY DIFFRACTION98.89

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