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- PDB-8vq0: UIC-13-MER extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vq0
TitleUIC-13-MER extension of UIC-1
ComponentsUIC-13-MER
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyMETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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-13-MER
B: UIC-13-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4323
Polymers3,4002
Non-polymers321
Water1629
1
A: UIC-13-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7322
Polymers1,7001
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-13-MER


Theoretical massNumber of molelcules
Total (without water)1,7001
Polymers1,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.356, 8.780, 44.935
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide UIC-13-MER


Mass: 1699.995 Da / Num. of mol.: 2 / 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.: 9 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: methanol, 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: 1.31→14.9 Å / Num. obs: 5489 / % possible obs: 96.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.25 Å2 / CC1/2: 1 / Net I/σ(I): 23.37
Reflection shellResolution: 1.31→1.357 Å / Num. unique obs: 457 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→14.9 Å / SU ML: 0.0834 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 980 9.93 %
Rwork0.1665 8889 -
obs0.1722 5489 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.43 Å2
Refinement stepCycle: LAST / Resolution: 1.31→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms168 0 78 9 255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088247
X-RAY DIFFRACTIONf_angle_d1.8139352
X-RAY DIFFRACTIONf_chiral_restr0.060120
X-RAY DIFFRACTIONf_plane_restr0.006340
X-RAY DIFFRACTIONf_dihedral_angle_d29.594242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.380.22511300.20111189X-RAY DIFFRACTION89.97
1.38-1.470.30271480.20861347X-RAY DIFFRACTION97.9
1.47-1.580.31571350.1951235X-RAY DIFFRACTION98.28
1.58-1.740.23231450.1951320X-RAY DIFFRACTION97.34
1.74-1.990.22291310.19071205X-RAY DIFFRACTION95.22
1.99-2.510.19711500.16491303X-RAY DIFFRACTION98.98
2.51-14.90.18981410.14451290X-RAY DIFFRACTION97.35

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