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- PDB-8vpd: UIC-11-BIF extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vpd
TitleUIC-11-BIF extension of UIC-1
ComponentsUIC-11-BIF
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
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-11-BIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5142
Polymers1,4731
Non-polymers411
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.485, 8.794, 31.786
Angle α, β, γ (deg.)90.000, 113.900, 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-11-BIF


Mass: 1472.732 Da / Num. of mol.: 1 / 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.: 10 / 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: 1.93 Å3/Da / Density % sol: 36.14 %
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: 0.688839 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688839 Å / Relative weight: 1
ReflectionResolution: 1.2→14.53 Å / Num. obs: 3163 / % possible obs: 95.61 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.21 Å2 / CC1/2: 0.984 / Net I/σ(I): 4.26
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 276 / CC1/2: 0.782

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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→14.53 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.0735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 559 9.82 %
Rwork0.2081 5135 -
obs0.21 3163 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.32 Å2
Refinement stepCycle: LAST / Resolution: 1.2→14.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms87 0 22 10 119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102118
X-RAY DIFFRACTIONf_angle_d1.8145167
X-RAY DIFFRACTIONf_chiral_restr0.044611
X-RAY DIFFRACTIONf_plane_restr0.008419
X-RAY DIFFRACTIONf_dihedral_angle_d30.803322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.320.41231320.35231197X-RAY DIFFRACTION88.01
1.32-1.510.28371420.27911336X-RAY DIFFRACTION97.82
1.51-1.90.22781390.23541283X-RAY DIFFRACTION97.06
1.91-14.530.18871460.15581319X-RAY DIFFRACTION97.54

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