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- PDB-8vt8: UIC-13-BIF-A4Dab NBD-Cl binding -

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Basic information

Entry
Database: PDB / ID: 8vt8
TitleUIC-13-BIF-A4Dab NBD-Cl binding
ComponentsUIC-13-BIF-A4Dab-NBD-Cl
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology4-chloro-7-nitrobenzofurazan / ACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 26, 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-BIF-A4Dab-NBD-Cl
B: UIC-13-BIF-A4Dab-NBD-Cl
C: UIC-13-BIF-A4Dab-NBD-Cl
D: UIC-13-BIF-A4Dab-NBD-Cl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1138
Polymers6,6324
Non-polymers4814
Water1629
1
A: UIC-13-BIF-A4Dab-NBD-Cl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8582
Polymers1,6581
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-13-BIF-A4Dab-NBD-Cl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8993
Polymers1,6581
Non-polymers2412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UIC-13-BIF-A4Dab-NBD-Cl


Theoretical massNumber of molelcules
Total (without water)1,6581
Polymers1,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UIC-13-BIF-A4Dab-NBD-Cl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6992
Polymers1,6581
Non-polymers411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.753, 18.836, 47.762
Angle α, β, γ (deg.)90.000, 98.880, 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-13-BIF-A4Dab-NBD-Cl


Mass: 1657.955 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-5Z8 / 4-chloro-7-nitrobenzofurazan / 4-chloranyl-7-nitro-2,1,3-benzoxadiazole / NBD-Cl / 4-nitro-2,1,3-benzoxadiazole (post-reaction)


Mass: 199.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H2ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#4: 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: 1.81 Å3/Da / Density % sol: 31.87 %
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: 0.72926 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: 0.72926 Å / Relative weight: 1
ReflectionResolution: 1.53→22.44 Å / Num. obs: 6463 / % possible obs: 98.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 23.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 6.04
Reflection shellResolution: 1.53→1.585 Å / Num. unique obs: 597 / CC1/2: 0.288

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→22.44 Å / SU ML: 0.309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.9376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2235 1207 10.06 %
Rwork0.1815 10793 -
obs0.1853 6463 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.81 Å2
Refinement stepCycle: LAST / Resolution: 1.53→22.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 106 9 515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012520
X-RAY DIFFRACTIONf_angle_d1.6058737
X-RAY DIFFRACTIONf_chiral_restr0.046441
X-RAY DIFFRACTIONf_plane_restr0.007383
X-RAY DIFFRACTIONf_dihedral_angle_d32.470798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.590.45391230.43981053X-RAY DIFFRACTION83.64
1.59-1.660.46591310.42491157X-RAY DIFFRACTION96.77
1.66-1.750.36011360.35181236X-RAY DIFFRACTION99.71
1.75-1.860.31561370.27781235X-RAY DIFFRACTION99.85
1.86-20.24191340.24171218X-RAY DIFFRACTION99.41
2-2.210.23241390.19231231X-RAY DIFFRACTION99.2
2.21-2.520.18231380.17191226X-RAY DIFFRACTION99.27
2.53-3.180.1861340.15551230X-RAY DIFFRACTION99.49
3.18-22.440.18741350.12031207X-RAY DIFFRACTION97.74

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