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- PDB-8vpy: UIC-16-MER extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vpy
TitleUIC-16-MER extension of UIC-1
ComponentsUIC-16-MER
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyMETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 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 17, 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-16-MER
B: UIC-16-MER
C: UIC-16-MER
D: UIC-16-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,19814
Polymers7,8774
Non-polymers32010
Water45025
1
A: UIC-16-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0333
Polymers1,9691
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-16-MER
hetero molecules


  • defined by author
  • 2.03 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,0333
Polymers1,9691
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UIC-16-MER
hetero molecules


  • defined by author
  • 2.13 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,1306
Polymers1,9691
Non-polymers1605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UIC-16-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0012
Polymers1,9691
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.434, 22.492, 31.230
Angle α, β, γ (deg.)104.440, 90.220, 104.740
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-16-MER


Mass: 1969.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: methanol and 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: 1.21→21.01 Å / Num. obs: 16793 / % possible obs: 96.31 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.63
Reflection shellResolution: 1.21→1.253 Å / Num. unique obs: 1682 / CC1/2: 0.474

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→21.01 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.1842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 3213 9.98 %
Rwork0.2014 28982 -
obs0.2064 16793 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.61 Å2
Refinement stepCycle: LAST / Resolution: 1.21→21.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms412 0 172 25 609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0106597
X-RAY DIFFRACTIONf_angle_d1.725844
X-RAY DIFFRACTIONf_chiral_restr0.04656
X-RAY DIFFRACTIONf_plane_restr0.007696
X-RAY DIFFRACTIONf_dihedral_angle_d30.9752106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.41131360.3631252X-RAY DIFFRACTION91.8
1.23-1.250.41281480.35921329X-RAY DIFFRACTION90.84
1.25-1.270.38611310.3731187X-RAY DIFFRACTION92.95
1.27-1.290.38821360.34941233X-RAY DIFFRACTION91.63
1.29-1.310.39641470.33381317X-RAY DIFFRACTION92.31
1.31-1.340.34291350.3171214X-RAY DIFFRACTION92.91
1.34-1.370.31681360.30551282X-RAY DIFFRACTION91.84
1.37-1.40.35821410.27571235X-RAY DIFFRACTION92.1
1.4-1.430.3671410.26191297X-RAY DIFFRACTION93.74
1.43-1.460.34341340.28231224X-RAY DIFFRACTION92.89
1.46-1.50.28111490.23481283X-RAY DIFFRACTION91.56
1.5-1.550.27871360.23621237X-RAY DIFFRACTION91.78
1.55-1.60.24661400.19781271X-RAY DIFFRACTION90.45
1.6-1.650.27441370.19751199X-RAY DIFFRACTION92.91
1.65-1.720.25081420.18761306X-RAY DIFFRACTION92.82
1.72-1.80.1951340.1841209X-RAY DIFFRACTION92.37
1.8-1.890.26861460.17341302X-RAY DIFFRACTION93.18
1.89-2.010.22081360.15711243X-RAY DIFFRACTION91.69
2.01-2.170.18771420.14381256X-RAY DIFFRACTION93.2
2.17-2.390.19081440.16331295X-RAY DIFFRACTION94.05
2.39-2.730.19121410.14781276X-RAY DIFFRACTION92.86
2.73-3.430.22481400.17491266X-RAY DIFFRACTION93.36
3.44-21.010.23771410.1991269X-RAY DIFFRACTION93.25

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