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- PDB-9c05: UIC-1 soaked in equimolar benzene, toluene, isopropylbenzene, and... -

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Basic information

Entry
Database: PDB / ID: 9c05
TitleUIC-1 soaked in equimolar benzene, toluene, isopropylbenzene, and ortho-xylene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyBENZENE / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / 5-METHYL-2-(1-METHYLETHYL)PHENOL / ORTHO-XYLENE / PHENYLETHANE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 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)1,9738
Polymers8971
Non-polymers1,0767
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.853, 13.330, 28.670
Angle α, β, γ (deg.)90.000, 90.730, 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 , 7 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
#5: Chemical ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#6: Chemical ChemComp-IPB / 5-METHYL-2-(1-METHYLETHYL)PHENOL


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.5 Å3/Da / Density % sol: 17.83 %
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: 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: 0.97→12.09 Å / Num. obs: 6310 / % possible obs: 98.35 % / Redundancy: 6.5 % / Biso Wilson estimate: 7.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.33
Reflection shellResolution: 0.97→1.005 Å / Num. unique obs: 627 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→12.09 Å / SU ML: 0.0563 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.7806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1112 1165 9.81 %
Rwork0.0973 10713 -
obs0.0991 6310 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.87 Å2
Refinement stepCycle: LAST / Resolution: 0.97→12.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 58 2 141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101196
X-RAY DIFFRACTIONf_angle_d1.9829261
X-RAY DIFFRACTIONf_chiral_restr0.048110
X-RAY DIFFRACTIONf_plane_restr0.007330
X-RAY DIFFRACTIONf_dihedral_angle_d39.31930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-1.010.19491450.15011350X-RAY DIFFRACTION97.46
1.01-1.070.15021370.11851371X-RAY DIFFRACTION98.63
1.07-1.130.10831520.10811335X-RAY DIFFRACTION98.87
1.13-1.220.12611440.09231353X-RAY DIFFRACTION98.62
1.22-1.340.09851401336X-RAY DIFFRACTION97.49
1.34-1.540.11141460.1011359X-RAY DIFFRACTION99.21
1.54-1.940.08421480.0951306X-RAY DIFFRACTION94.91
1.94-12.090.11011530.08691303X-RAY DIFFRACTION96.62

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