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- PDB-8vw8: UIC-13-BPE-AgNO3 silver binding with UIC-13-BPE -

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Basic information

Entry
Database: PDB / ID: 8vw8
TitleUIC-13-BPE-AgNO3 silver binding with UIC-13-BPE
ComponentsUIC-13-BPE-AgNO3 silver binding with UIC-13-BPE
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologySILVER ION / NITRATE ION
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 31, 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

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Assembly

Deposited unit
A: UIC-13-BPE-AgNO3 silver binding with UIC-13-BPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8573
Polymers1,6871
Non-polymers1702
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.634, 59.634, 9.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-102-

NO3

21A-207-

HOH

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Components

#1: Protein/peptide UIC-13-BPE-AgNO3 silver binding with UIC-13-BPE


Mass: 1686.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: 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: 2.95 Å3/Da / Density % sol: 58.33 %
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: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.2→18.86 Å / Num. obs: 5566 / % possible obs: 99.5 % / Redundancy: 24.3 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.74
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 542 / CC1/2: 0.533

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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→18.86 Å / SU ML: 0.1469 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 977 10.06 %
Rwork0.1897 8734 -
obs0.1932 5566 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.98 Å2
Refinement stepCycle: LAST / Resolution: 1.2→18.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms103 0 24 10 137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0288149
X-RAY DIFFRACTIONf_angle_d1.7894208
X-RAY DIFFRACTIONf_chiral_restr0.028810
X-RAY DIFFRACTIONf_plane_restr0.010225
X-RAY DIFFRACTIONf_dihedral_angle_d36.995929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.260.34961450.36311269X-RAY DIFFRACTION99.93
1.26-1.340.37371350.33961239X-RAY DIFFRACTION99.64
1.34-1.450.3251390.28671243X-RAY DIFFRACTION99.93
1.45-1.590.28131340.24891245X-RAY DIFFRACTION99.93
1.59-1.820.25321420.22331279X-RAY DIFFRACTION99.93
1.82-2.290.1641390.15761234X-RAY DIFFRACTION99.56
2.3-18.860.19441430.14011225X-RAY DIFFRACTION99.35

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