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- PDB-9bzz: UIC-1 peptide bound with ethylbenzene -

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Basic information

Entry
Database: PDB / ID: 9bzz
TitleUIC-1 peptide bound with ethylbenzene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / PHENYLETHANE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 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

Downloads & links

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Assembly

Deposited unit
A: UIC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8517
Polymers8971
Non-polymers9546
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.986, 13.532, 28.790
Angle α, β, γ (deg.)90.000, 101.000, 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-PYJ / PHENYLETHANE


Mass: 106.165 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10 / 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: 1.46 Å3/Da / Density % sol: 15.56 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: acetonitrile and 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: 0.688839 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688839 Å / Relative weight: 1
ReflectionResolution: 0.81→13.73 Å / Num. obs: 10819 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 4.81 Å2 / CC1/2: 0.997 / Net I/σ(I): 19.17
Reflection shellResolution: 0.81→0.839 Å / Num. unique obs: 1072 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.81→13.73 Å / SU ML: 0.0331 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.3799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1024 2052 10.1 %
Rwork0.0991 18273 -
obs0.0995 10819 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.47 Å2
Refinement stepCycle: LAST / Resolution: 0.81→13.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 51 0 132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172250
X-RAY DIFFRACTIONf_angle_d3.0808329
X-RAY DIFFRACTIONf_chiral_restr0.049114
X-RAY DIFFRACTIONf_plane_restr0.012638
X-RAY DIFFRACTIONf_dihedral_angle_d39.381542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.81-0.830.14021290.14021158X-RAY DIFFRACTION94.91
0.83-0.850.16181230.12331274X-RAY DIFFRACTION95.55
0.85-0.870.14131500.11411203X-RAY DIFFRACTION96.57
0.87-0.90.12011310.10471197X-RAY DIFFRACTION95.82
0.9-0.930.12561520.10391220X-RAY DIFFRACTION96.15
0.93-0.960.10281290.09941204X-RAY DIFFRACTION96.18
0.96-10.09061280.08861207X-RAY DIFFRACTION94.28
1-1.040.10531240.07821196X-RAY DIFFRACTION94.15
1.04-1.10.09241510.07891220X-RAY DIFFRACTION98.42
1.1-1.170.08661450.07931244X-RAY DIFFRACTION98.51
1.17-1.260.09991370.07751232X-RAY DIFFRACTION98.42
1.26-1.380.09411380.08771262X-RAY DIFFRACTION97.43
1.38-1.580.09451340.10111182X-RAY DIFFRACTION96.41
1.59-20.1071420.10621220X-RAY DIFFRACTION94.78
2-13.730.09811390.11241254X-RAY DIFFRACTION99.86

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