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- PDB-9c00: UIC-1 soaked with R/S 1-chloroethylbenzene -

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Basic information

Entry
Database: PDB / ID: 9c00
TitleUIC-1 soaked with R/S 1-chloroethylbenzene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology: / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.9 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)1,7085
Polymers8971
Non-polymers8114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.976, 13.458, 28.590
Angle α, β, γ (deg.)90.000, 90.190, 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-A1ATC / [(1S)-1-chloroethyl]benzene


Mass: 140.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9Cl / 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: 1.6 Å3/Da / Density % sol: 23.04 %
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 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 0.9→14.3 Å / Num. obs: 8119 / % possible obs: 99.75 % / Redundancy: 9.1 % / Biso Wilson estimate: 8.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.19
Reflection shellResolution: 0.9→0.9322 Å / Num. unique obs: 818 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.9→14.3 Å / SU ML: 0.1141 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 798 9.85 %
Rwork0.1793 7302 -
obs0.1827 8100 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.03 Å2
Refinement stepCycle: LAST / Resolution: 0.9→14.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 37 0 118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113176
X-RAY DIFFRACTIONf_angle_d1.89239
X-RAY DIFFRACTIONf_chiral_restr0.035413
X-RAY DIFFRACTIONf_plane_restr0.007127
X-RAY DIFFRACTIONf_dihedral_angle_d38.116338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.960.38721250.33391208X-RAY DIFFRACTION99.03
0.96-1.030.2821350.2491199X-RAY DIFFRACTION100
1.03-1.130.22981300.20271204X-RAY DIFFRACTION100
1.13-1.30.19931280.15791217X-RAY DIFFRACTION100
1.3-1.630.19811400.17121214X-RAY DIFFRACTION100
1.64-14.30.19691400.15941260X-RAY DIFFRACTION99.57

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