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- PDB-8tnc: De novo designed protein binds poly ADP ribose polymerase inhibit... -

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Basic information

Entry
Database: PDB / ID: 8tnc
TitleDe novo designed protein binds poly ADP ribose polymerase inhibitors (PARPi) - holo niraparib
ComponentsDe novo designed protein
KeywordsDE NOVO PROTEIN / drug binding / 4-helix bundle / de novo design / PARPi
Function / homologyChem-3JD
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLu, L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM122603 United States
CitationJournal: Science / Year: 2024
Title: De novo design of drug-binding proteins with predictable binding energy and specificity.
Authors: Lu, L. / Gou, X. / Tan, S.K. / Mann, S.I. / Yang, H. / Zhong, X. / Gazgalis, D. / Valdiviezo, J. / Jo, H. / Wu, Y. / Diolaiti, M.E. / Ashworth, A. / Polizzi, N.F. / DeGrado, W.F.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed protein
B: De novo designed protein
C: De novo designed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5736
Polymers48,6123
Non-polymers9613
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.007, 91.007, 203.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

21B-318-

HOH

31B-320-

HOH

41B-347-

HOH

51B-375-

HOH

61C-307-

HOH

71C-353-

HOH

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Components

#1: Protein De novo designed protein


Mass: 16203.947 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-3JD / 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide / Niraparib


Mass: 320.388 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H20N4O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.39→203.65 Å / Num. obs: 99665 / % possible obs: 99.8 % / Redundancy: 37 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.028 / Χ2: 0.97 / Net I/σ(I): 17
Reflection shellResolution: 1.39→1.42 Å / Num. unique obs: 4668 / CC1/2: 0.212

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIXrefinerefinement
XDSdata reduction
pointlessdata scaling
PHASERPhaserphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→78.81 Å / SU ML: 0.1957 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 2000 2.02 %
Rwork0.202 97171 -
obs0.2024 99171 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→78.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 72 269 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823534
X-RAY DIFFRACTIONf_angle_d0.90834788
X-RAY DIFFRACTIONf_chiral_restr0.0565561
X-RAY DIFFRACTIONf_plane_restr0.0074624
X-RAY DIFFRACTIONf_dihedral_angle_d7.2397492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.38491360.36516592X-RAY DIFFRACTION96.72
1.43-1.470.29851410.29776884X-RAY DIFFRACTION100
1.47-1.510.27461400.25136807X-RAY DIFFRACTION100
1.51-1.560.26571420.24646870X-RAY DIFFRACTION100
1.56-1.620.24141410.22876861X-RAY DIFFRACTION100
1.62-1.680.29051410.23676876X-RAY DIFFRACTION100
1.68-1.760.33131420.2556886X-RAY DIFFRACTION99.96
1.76-1.850.28521420.23316896X-RAY DIFFRACTION99.96
1.85-1.970.22471430.20776923X-RAY DIFFRACTION99.97
1.97-2.120.21261430.18756962X-RAY DIFFRACTION100
2.12-2.330.17661440.16096991X-RAY DIFFRACTION100
2.33-2.670.21311440.16527030X-RAY DIFFRACTION100
2.67-3.360.21241470.1847114X-RAY DIFFRACTION100
3.36-78.810.21611540.20977479X-RAY DIFFRACTION99.75

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