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- PDB-9bzt: UIC-1 bound to benzene -

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Basic information

Entry
Database: PDB / ID: 9bzt
TitleUIC-1 bound to benzene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyBENZENE / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.82 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)1,6616
Polymers8971
Non-polymers7645
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)14.128, 13.313, 27.459
Angle α, β, γ (deg.)90.000, 98.830, 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-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 1.56 Å3/Da / Density % sol: 21.26 %
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: 0.688839 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: 0.82→13.27 Å / Num. obs: 9542 / % possible obs: 94.04 % / Redundancy: 5.7 % / Biso Wilson estimate: 4.81 Å2 / CC1/2: 0.88 / Net I/σ(I): 9.54
Reflection shellResolution: 0.82→0.8494 Å / Num. unique obs: 5914 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.82→13.27 Å / SU ML: 0.0611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1731 1759 9.95 %
Rwork0.16 15926 -
obs0.1613 17685 91.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.42 Å2
Refinement stepCycle: LAST / Resolution: 0.82→13.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 37 1 119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011141
X-RAY DIFFRACTIONf_angle_d2.0519188
X-RAY DIFFRACTIONf_chiral_restr0.053912
X-RAY DIFFRACTIONf_plane_restr0.008222
X-RAY DIFFRACTIONf_dihedral_angle_d34.758521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.82-0.840.22121490.18961325X-RAY DIFFRACTION97.49
0.84-0.870.20261380.17721278X-RAY DIFFRACTION96.66
0.87-0.90.19381420.16511298X-RAY DIFFRACTION96.84
0.9-0.930.16881470.16441304X-RAY DIFFRACTION97.78
0.93-0.960.13451470.15441331X-RAY DIFFRACTION97.49
0.96-1.010.16171430.14211253X-RAY DIFFRACTION92.76
1.01-1.060.14261280.12641172X-RAY DIFFRACTION88.92
1.06-1.130.16011460.12111294X-RAY DIFFRACTION97.1
1.13-1.210.1321410.1271326X-RAY DIFFRACTION96.64
1.21-1.340.13521400.13871247X-RAY DIFFRACTION95.59
1.34-1.530.14181360.14831257X-RAY DIFFRACTION92.68
1.53-1.850.1643940.1599876X-RAY DIFFRACTION74.22
1.98-13.270.23791080.2069965X-RAY DIFFRACTION77.81

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