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- PDB-9c06: UIC-1 A4S/B5(4-Cl)F soaked in equimolar ortho-, meta-, and para-xylene -

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Basic information

Entry
Database: PDB / ID: 9c06
TitleUIC-1 A4S/B5(4-Cl)F soaked in equimolar ortho-, meta-, and para-xylene
ComponentsUIC-1-A4S/B5F(4-Cl)/B7M
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyethyl 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: 0.85 Å
AuthorsHeinz-Kunert, S.L. / Nguyen, A.I.
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-A4S/B5F(4-Cl)/B7M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9046
Polymers1,0561
Non-polymers8485
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)13.553, 13.461, 30.458
Angle α, β, γ (deg.)90.000, 95.000, 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-A4S/B5F(4-Cl)/B7M


Mass: 1055.719 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-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10 / 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: 1.44 Å3/Da / Density % sol: 14.58 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.688802 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688802 Å / Relative weight: 1
ReflectionResolution: 0.85→10.07 Å / Num. obs: 9835 / % possible obs: 99.33 % / Redundancy: 6.4 % / Biso Wilson estimate: 8.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 35.73
Reflection shellResolution: 0.85→0.8804 Å / Num. unique obs: 961 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.85→10.07 Å / SU ML: 0.059 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.0172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1375 968 -
Rwork0.1375 0 -
obs0.1375 9835 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.38 Å2
Refinement stepCycle: LAST / Resolution: 0.85→10.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90 0 43 0 133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0104170
X-RAY DIFFRACTIONf_angle_d1.6133228
X-RAY DIFFRACTIONf_chiral_restr0.150711
X-RAY DIFFRACTIONf_plane_restr0.005826
X-RAY DIFFRACTIONf_dihedral_angle_d40.71624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.860.24676250.2467625X-RAY DIFFRACTION99.52
0.86-0.870.24916270.2491627X-RAY DIFFRACTION99.68
0.87-0.880.23046100.2304610X-RAY DIFFRACTION99.19
0.88-0.890.22956380.2295638X-RAY DIFFRACTION98.61
0.89-0.90.21866460.2186646X-RAY DIFFRACTION98.78
0.9-0.920.24226180.2422618X-RAY DIFFRACTION99.2
0.92-0.930.2255790.225579X-RAY DIFFRACTION98.81
0.93-0.940.20926330.2092633X-RAY DIFFRACTION99.22
0.94-0.960.19746600.1974660X-RAY DIFFRACTION99.85
0.96-0.970.19416480.1941648X-RAY DIFFRACTION100
0.97-0.990.19435690.1943569X-RAY DIFFRACTION100
0.99-1.010.18556620.1855662X-RAY DIFFRACTION100
1.01-1.030.18776160.1877616X-RAY DIFFRACTION100
1.03-1.050.16536540.1653654X-RAY DIFFRACTION100
1.05-1.070.16646080.1664608X-RAY DIFFRACTION99.84
1.07-1.10.16866090.1686609X-RAY DIFFRACTION99.67
1.1-1.120.14166960.1416696X-RAY DIFFRACTION99.29
1.12-1.150.16355600.1635560X-RAY DIFFRACTION98.25
1.15-1.190.13236360.1323636X-RAY DIFFRACTION99.38
1.19-1.230.13476360.1347636X-RAY DIFFRACTION100
1.23-1.270.15176140.1517614X-RAY DIFFRACTION99.68
1.27-1.320.13086370.1308637X-RAY DIFFRACTION100
1.32-1.380.13436150.1343615X-RAY DIFFRACTION98.72
1.38-1.450.13086200.1308620X-RAY DIFFRACTION99.52
1.45-1.540.14446120.1444612X-RAY DIFFRACTION99.67
1.54-1.660.11826500.1182650X-RAY DIFFRACTION99.85
1.66-1.830.11646070.1164607X-RAY DIFFRACTION99.02
1.83-2.090.10076310.1007631X-RAY DIFFRACTION99.84
2.09-2.630.1086300.108630X-RAY DIFFRACTION98.75
2.63-10.070.13135920.1313592X-RAY DIFFRACTION93.67

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