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- PDB-8vpz: UIC-1-BPE1MER mutation of UIC-1-cap -

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Basic information

Entry
Database: PDB / ID: 8vpz
TitleUIC-1-BPE1MER mutation of UIC-1-cap
ComponentsUIC-1-BPE1MER
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyMETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 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-1-BPE1MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4202
Polymers1,3881
Non-polymers321
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.643, 9.082, 27.945
Angle α, β, γ (deg.)90.000, 98.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide UIC-1-BPE1MER


Mass: 1387.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: methanol, water, acetonitrile

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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 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.04→11.49 Å / Num. obs: 4131 / % possible obs: 97.65 % / Redundancy: 6.5 % / Biso Wilson estimate: 5.04 Å2 / CC1/2: 0.99 / Net I/σ(I): 44.12
Reflection shellResolution: 1.04→1.077 Å / Num. unique obs: 399 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→11.49 Å / SU ML: 0.0455 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 10.3239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.101 751 9.92 %
Rwork0.0863 6820 -
obs0.0876 4131 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.28 Å2
Refinement stepCycle: LAST / Resolution: 1.04→11.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62 0 40 2 104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126172
X-RAY DIFFRACTIONf_angle_d2.0134236
X-RAY DIFFRACTIONf_chiral_restr0.08139
X-RAY DIFFRACTIONf_plane_restr0.010429
X-RAY DIFFRACTIONf_dihedral_angle_d40.488823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.120.09631570.07891389X-RAY DIFFRACTION98.53
1.12-1.230.1111450.07411334X-RAY DIFFRACTION96.98
1.23-1.410.10381500.08241348X-RAY DIFFRACTION97.21
1.41-1.780.09971520.08981420X-RAY DIFFRACTION99.68
1.78-11.490.09821470.09181329X-RAY DIFFRACTION95.35

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