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- PDB-8vpc: UIC-13-BIF extension of UIC-1 -

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Basic information

Entry
Database: PDB / ID: 8vpc
TitleUIC-13-BIF extension of UIC-1
ComponentsUIC-13-BIF
KeywordsDE NOVO PROTEIN / synthetic construct
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 16, 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-BIF
B: UIC-13-BIF
C: UIC-13-BIF
D: UIC-13-BIF


Theoretical massNumber of molelcules
Total (without water)6,5164
Polymers6,5164
Non-polymers00
Water77543
1
A: UIC-13-BIF


Theoretical massNumber of molelcules
Total (without water)1,6291
Polymers1,6291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-13-BIF


Theoretical massNumber of molelcules
Total (without water)1,6291
Polymers1,6291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UIC-13-BIF


Theoretical massNumber of molelcules
Total (without water)1,6291
Polymers1,6291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UIC-13-BIF


Theoretical massNumber of molelcules
Total (without water)1,6291
Polymers1,6291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.960, 23.781, 23.831
Angle α, β, γ (deg.)103.870, 106.560, 106.460
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-13-BIF


Mass: 1628.914 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.96 Å3/Da / Density % sol: 37.12 %
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: 0.72925 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72925 Å / Relative weight: 1
ReflectionResolution: 0.94→21.38 Å / Num. obs: 24348 / % possible obs: 86.07 % / Redundancy: 3.5 % / Biso Wilson estimate: 5.17 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.15
Reflection shellResolution: 0.94→0.9736 Å / Num. unique obs: 2504 / CC1/2: 0.932

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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→21.38 Å / SU ML: 0.1332 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.3837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 3519 7.66 %
Rwork0.2047 42409 -
obs0.2063 24348 81.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.5 Å2
Refinement stepCycle: LAST / Resolution: 0.94→21.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms392 0 76 43 511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085492
X-RAY DIFFRACTIONf_angle_d1.6917703
X-RAY DIFFRACTIONf_chiral_restr0.031340
X-RAY DIFFRACTIONf_plane_restr0.00780
X-RAY DIFFRACTIONf_dihedral_angle_d33.357293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.950.43531680.33781829X-RAY DIFFRACTION86.98
0.95-0.970.36561560.29971694X-RAY DIFFRACTION84.4
0.97-0.980.24581350.27651802X-RAY DIFFRACTION86.17
0.98-10.21741620.23511759X-RAY DIFFRACTION84.03
1-1.010.25031360.20971733X-RAY DIFFRACTION82.99
1.01-1.030.2411640.20641724X-RAY DIFFRACTION84.06
1.03-1.050.22091150.19751763X-RAY DIFFRACTION84.37
1.05-1.070.24451640.20521686X-RAY DIFFRACTION80.93
1.07-1.090.2431520.20661745X-RAY DIFFRACTION83.27
1.09-1.110.241630.18571665X-RAY DIFFRACTION81.03
1.11-1.140.18891130.17941756X-RAY DIFFRACTION81.33
1.14-1.170.19791490.16261617X-RAY DIFFRACTION78.77
1.17-1.20.23461370.18061672X-RAY DIFFRACTION80.26
1.2-1.240.20581330.16621593X-RAY DIFFRACTION78.67
1.24-1.280.21721480.17981703X-RAY DIFFRACTION79.58
1.28-1.320.2191400.18011676X-RAY DIFFRACTION78.96
1.32-1.370.18111320.18131581X-RAY DIFFRACTION77.51
1.37-1.440.18851380.20461635X-RAY DIFFRACTION79.01
1.44-1.510.22551190.19441662X-RAY DIFFRACTION79.16
1.51-1.610.27341300.20281607X-RAY DIFFRACTION76.25
1.61-1.730.22291340.21041622X-RAY DIFFRACTION76.35
1.73-1.910.21121170.2121637X-RAY DIFFRACTION78.65
1.91-2.180.19891340.21041691X-RAY DIFFRACTION80.04
2.18-2.750.22051500.21031685X-RAY DIFFRACTION81.92
2.75-21.380.23551300.21421872X-RAY DIFFRACTION88.19

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