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- PDB-9c02: UIC-1 B7M soaked with equimolar ortho-, meta-, and para-xylene -

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Basic information

Entry
Database: PDB / ID: 9c02
TitleUIC-1 B7M soaked with equimolar ortho-, meta-, and para-xylene
ComponentsUIC-1
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology1,3-dimethylbenzene / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / ORTHO-XYLENE
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)1,8977
Polymers9431
Non-polymers9546
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)13.789, 13.388, 27.130
Angle α, β, γ (deg.)90.000, 97.660, 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: 943.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 8 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-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-8VH / 1,3-dimethylbenzene


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
#6: 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: 1.37 Å3/Da / Density % sol: 9.9 %
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: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688801 Å / Relative weight: 1
ReflectionResolution: 0.97→12.9 Å / Num. obs: 5048 / % possible obs: 84.07 % / Redundancy: 6.3 % / Biso Wilson estimate: 5.66 Å2 / CC1/2: 0.999 / Net I/σ(I): 28.55
Reflection shellResolution: 0.97→1.005 Å / Num. unique obs: 442 / CC1/2: 0.999

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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→12.9 Å / SU ML: 0.061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1 950 10.1 %
Rwork0.081 8455 -
obs0.0986 5048 82.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.29 Å2
Refinement stepCycle: LAST / Resolution: 0.97→12.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms83 0 51 2 136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125172
X-RAY DIFFRACTIONf_angle_d1.8565232
X-RAY DIFFRACTIONf_chiral_restr0.068912
X-RAY DIFFRACTIONf_plane_restr0.00726
X-RAY DIFFRACTIONf_dihedral_angle_d37.187425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-1.020.13531140.10251007X-RAY DIFFRACTION69.63
1.02-1.090.12271250.09241113X-RAY DIFFRACTION76.51
1.09-1.160.11021460.07271279X-RAY DIFFRACTION91.58
1.17-1.290.0961430.07641269X-RAY DIFFRACTION87.54
1.29-1.470.09131290.07881182X-RAY DIFFRACTION80.93
1.47-1.850.1031550.0771336X-RAY DIFFRACTION92.61
1.85-12.90.09111380.08281269X-RAY DIFFRACTION85.74

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