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- PDB-9bzu: UIC-1 peptide with toluene bound -

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Basic information

Entry
Database: PDB / ID: 9bzu
TitleUIC-1 peptide with toluene bound
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / TOLUENE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsHeinz-Kunert, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: To Be Published
Title: Evolvable conformational diversity in assemblies of short peptides
Authors: Heinz-Kunert, S.L. / Nguyen, A.I.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UIC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7957
Polymers8971
Non-polymers8986
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.966, 13.451, 28.645
Angle α, β, γ (deg.)90.000, 101.480, 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


Mass: 897.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-I77 / 5'-(hydrazinecarbonyl)[2,2'-bipyridine]-5-carboxamide


Mass: 257.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-I6W / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate


Mass: 272.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 1.49 Å3/Da / Density % sol: 17.51 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water and 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: 0.61986 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61986 Å / Relative weight: 1
ReflectionResolution: 0.92→14.04 Å / Num. obs: 7211 / % possible obs: 96.71 % / Redundancy: 6.2 % / Biso Wilson estimate: 6.3 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.88
Reflection shellResolution: 0.92→0.9529 Å / Num. unique obs: 4164 / CC1/2: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.92→14.04 Å / SU ML: 0.0648 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 16.6589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1294 1305 9.84 %
Rwork0.1163 11951 -
obs0.1176 7211 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.85 Å2
Refinement stepCycle: LAST / Resolution: 0.92→14.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 47 0 128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125222
X-RAY DIFFRACTIONf_angle_d1.854295
X-RAY DIFFRACTIONf_chiral_restr0.046514
X-RAY DIFFRACTIONf_plane_restr0.006535
X-RAY DIFFRACTIONf_dihedral_angle_d36.073530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.960.20851290.19041284X-RAY DIFFRACTION89.66
0.96-10.1711390.15521348X-RAY DIFFRACTION94.96
1-1.050.15161400.14161316X-RAY DIFFRACTION93.15
1.05-1.120.14721460.12491348X-RAY DIFFRACTION93.03
1.12-1.210.17031470.11621303X-RAY DIFFRACTION92.42
1.21-1.330.14731540.11751281X-RAY DIFFRACTION91.99
1.33-1.520.14171460.11951373X-RAY DIFFRACTION95.59
1.52-1.910.09291580.11021358X-RAY DIFFRACTION95.83
1.91-14.040.11461460.10041340X-RAY DIFFRACTION95.2

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