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- PDB-8vog: UIC-12-BIF extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vog
TitleUIC-12-BIF extension of UIC-1
ComponentsUIC-12-BIF
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 15, 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-BIF
B: UIC-12-BIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2806
Polymers3,1162
Non-polymers1644
Water34219
1
A: UIC-12-BIF
hetero molecules


  • defined by author
  • 1.64 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,6403
Polymers1,5581
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-12-BIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6403
Polymers1,5581
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.240, 15.760, 31.197
Angle α, β, γ (deg.)95.870, 97.000, 90.090
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-12-BIF


Mass: 1557.836 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.: 4 / Source method: obtained synthetically / Formula: C2H3N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
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: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.94→15.68 Å / Num. obs: 11219 / % possible obs: 89.58 % / Redundancy: 3.7 % / Biso Wilson estimate: 4.65 Å2 / CC1/2: 0.958 / Net I/σ(I): 27.93
Reflection shellResolution: 0.94→0.9736 Å / Num. unique obs: 1138 / CC1/2: 0.995

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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→15.68 Å / SU ML: 0.0463 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 7.1563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.0898 2074 9.88 %
Rwork0.0786 18920 -
obs0.0799 11219 83.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.6 Å2
Refinement stepCycle: LAST / Resolution: 0.94→15.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms186 0 50 19 255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078274
X-RAY DIFFRACTIONf_angle_d1.8008385
X-RAY DIFFRACTIONf_chiral_restr0.037720
X-RAY DIFFRACTIONf_plane_restr0.006546
X-RAY DIFFRACTIONf_dihedral_angle_d30.886674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.960.09041410.08021297X-RAY DIFFRACTION89.99
0.96-0.990.08661580.07111372X-RAY DIFFRACTION88.85
0.99-1.010.10251350.07691188X-RAY DIFFRACTION81.97
1.01-1.040.09241390.07191405X-RAY DIFFRACTION89.56
1.04-1.080.07671520.07181268X-RAY DIFFRACTION86.8
1.08-1.110.08371210.06691279X-RAY DIFFRACTION81.59
1.11-1.160.08991440.0651203X-RAY DIFFRACTION82.64
1.16-1.210.07641340.06611235X-RAY DIFFRACTION82.07
1.21-1.280.09271210.07371091X-RAY DIFFRACTION71.38
1.28-1.360.07811450.07451343X-RAY DIFFRACTION90.51
1.36-1.460.07681560.07721333X-RAY DIFFRACTION85.87
1.46-1.610.07611400.07911270X-RAY DIFFRACTION87.36
1.61-1.840.10611290.08351255X-RAY DIFFRACTION82.09
1.84-2.320.09561270.08591131X-RAY DIFFRACTION75.69
2.32-15.680.09791320.08951250X-RAY DIFFRACTION82.56

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