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- PDB-8vpe: UIC-10-BIF extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vpe
TitleUIC-10-BIF extension of UIC-1
ComponentsUIC-10-BIF
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 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-10-BIF
B: UIC-10-BIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0919
Polymers2,8032
Non-polymers2877
Water19811
1
A: UIC-10-BIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5254
Polymers1,4021
Non-polymers1233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-10-BIF
hetero molecules


  • defined by author
  • 1.57 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5665
Polymers1,4021
Non-polymers1644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.764, 36.020, 47.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide UIC-10-BIF


Mass: 1401.654 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.: 7 / Source method: obtained synthetically / Formula: C2H3N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
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: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.91→16.84 Å / Num. obs: 13878 / % possible obs: 99.18 % / Redundancy: 12.8 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.69
Reflection shellResolution: 0.91→0.9426 Å / Num. unique obs: 1314 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.91→16.84 Å / SU ML: 0.0406 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 9.9221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1114 2520 9.93 %
Rwork0.095 22855 -
obs0.0965 13878 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.48 Å2
Refinement stepCycle: LAST / Resolution: 0.91→16.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms164 0 59 11 234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117256
X-RAY DIFFRACTIONf_angle_d1.9379352
X-RAY DIFFRACTIONf_chiral_restr0.078623
X-RAY DIFFRACTIONf_plane_restr0.015640
X-RAY DIFFRACTIONf_dihedral_angle_d29.06171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.91-0.930.17681380.14491194X-RAY DIFFRACTION94.54
0.93-0.950.16511460.13181283X-RAY DIFFRACTION100
0.95-0.970.12611490.11861301X-RAY DIFFRACTION99.93
0.97-0.990.13561400.1151280X-RAY DIFFRACTION100
0.99-1.010.12541370.10891231X-RAY DIFFRACTION100
1.01-1.040.09421480.10721273X-RAY DIFFRACTION99.93
1.04-1.070.12591420.10581334X-RAY DIFFRACTION99.8
1.07-1.110.11021270.10171226X-RAY DIFFRACTION99.12
1.11-1.150.09241410.08771285X-RAY DIFFRACTION100
1.15-1.190.10651420.08621307X-RAY DIFFRACTION99.04
1.19-1.250.09971320.08531197X-RAY DIFFRACTION96.94
1.25-1.310.10441420.0931306X-RAY DIFFRACTION99.86
1.31-1.390.12361430.09611259X-RAY DIFFRACTION99.86
1.39-1.50.12371420.09141289X-RAY DIFFRACTION100
1.5-1.650.10071340.09121258X-RAY DIFFRACTION99.93
1.65-1.890.08641380.08811301X-RAY DIFFRACTION99.79
1.89-2.380.08491360.08191241X-RAY DIFFRACTION98.08
2.38-16.840.13171430.09761290X-RAY DIFFRACTION100

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