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- PDB-9c04: UIC-1 soaked in equimolar toluene, para-xylene, and ethylbenzene -

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Basic information

Entry
Database: PDB / ID: 9c04
TitleUIC-1 soaked in equimolar toluene, para-xylene, and ethylbenzene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / TOLUENE / PARA-XYLENE / PHENYLETHANE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 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)2,0369
Polymers8971
Non-polymers1,1388
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.905, 13.424, 28.803
Angle α, β, γ (deg.)90.000, 101.510, 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

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide UIC-1


Mass: 897.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 9 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PXY / PARA-XYLENE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 17.43 %
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: MAX IV / Beamline: BioMAX / Wavelength: 0.688801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688801 Å / Relative weight: 1
ReflectionResolution: 0.94→13.63 Å / Num. obs: 6805 / % possible obs: 97.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 7.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 48.63
Reflection shellResolution: 0.94→0.9736 Å / Rmerge(I) obs: 0.08306 / Num. unique obs: 676 / CC1/2: 0.998 / CC star: 0.08996

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
X-GENdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.94→13.63 Å / SU ML: 0.0371 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1086 1289 10.04 %
Rwork0.0878 11550 -
obs0.0899 6805 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.2 Å2
Refinement stepCycle: LAST / Resolution: 0.94→13.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 65 1 147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121227
X-RAY DIFFRACTIONf_angle_d2.1915302
X-RAY DIFFRACTIONf_chiral_restr0.035714
X-RAY DIFFRACTIONf_plane_restr0.007535
X-RAY DIFFRACTIONf_dihedral_angle_d36.731533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.980.13431450.09651281X-RAY DIFFRACTION94.75
0.98-1.020.09661300.08591273X-RAY DIFFRACTION94.41
1.02-1.080.12661510.08281296X-RAY DIFFRACTION98.44
1.08-1.140.09361340.08111270X-RAY DIFFRACTION95.45
1.14-1.230.10541460.07531278X-RAY DIFFRACTION96.61
1.23-1.360.09661430.08341275X-RAY DIFFRACTION96.59
1.36-1.550.10121540.09081295X-RAY DIFFRACTION98.57
1.55-1.950.09241390.08951333X-RAY DIFFRACTION99.19
1.95-13.630.12141470.09151249X-RAY DIFFRACTION94.58

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