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- PDB-9c01: UIC-1 bound to phenol -

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Basic information

Entry
Database: PDB / ID: 9c01
TitleUIC-1 bound to phenol
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / PHENOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.83 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)1,5214
Polymers8971
Non-polymers6243
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.916, 13.389, 27.419
Angle α, β, γ (deg.)90.000, 98.750, 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-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.7 Å3/Da / Density % sol: 27.7 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 0.83→13.55 Å / Num. obs: 9671 / % possible obs: 99.91 % / Redundancy: 9.8 % / Biso Wilson estimate: 6.31 Å2 / CC1/2: 1 / Net I/σ(I): 40.19
Reflection shellResolution: 0.83→0.8597 Å / Num. unique obs: 946 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.83→13.55 Å / SU ML: 0.0339 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.2304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1162 967 10.01 %
Rwork0.0861 8698 -
obs-9665 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.36 Å2
Refinement stepCycle: LAST / Resolution: 0.83→13.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62 0 45 21 128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153218
X-RAY DIFFRACTIONf_angle_d2.2859301
X-RAY DIFFRACTIONf_chiral_restr0.036613
X-RAY DIFFRACTIONf_plane_restr0.009835
X-RAY DIFFRACTIONf_dihedral_angle_d44.218539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.83-0.870.13051370.10661231X-RAY DIFFRACTION100
0.87-0.930.11451350.09231220X-RAY DIFFRACTION100
0.93-10.10631370.07591229X-RAY DIFFRACTION100
1-1.10.08621380.06741234X-RAY DIFFRACTION100
1.1-1.260.08451370.06781249X-RAY DIFFRACTION99.93
1.26-1.590.11571390.09281243X-RAY DIFFRACTION100
1.59-13.550.13111440.09291292X-RAY DIFFRACTION99.58

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