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- PDB-8tn1: De novo designed protein binds poly ADP ribose polymerase inhibit... -

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Basic information

Entry
Database: PDB / ID: 8tn1
TitleDe novo designed protein binds poly ADP ribose polymerase inhibitors (PARPi) - apo
ComponentsDe novo designed 4 helix bundles
KeywordsDE NOVO PROTEIN / drug binding / 4-helix bundle / de novo design / PARPi
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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

Downloads & links

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Assembly

Deposited unit
A: De novo designed 4 helix bundles
B: De novo designed 4 helix bundles
C: De novo designed 4 helix bundles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9967
Polymers48,6123
Non-polymers3844
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.518, 90.518, 202.328
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-362-

HOH

21A-403-

HOH

31B-306-

HOH

41C-214-

HOH

51C-276-

HOH

61C-291-

HOH

71C-293-

HOH

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Components

#1: Protein De novo designed 4 helix bundles


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
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 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.61→78.39 Å / Num. obs: 61025 / % possible obs: 95.9 % / Redundancy: 20 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.015 / Rrim(I) all: 0.117 / Χ2: 0.85 / Net I/σ(I): 26.8
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 61437 / CC1/2: 0.092

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
PHENIXPhenix refinerefinement
Cootmodel building
PHENIXautobuildmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→78.39 Å / SU ML: 0.2769 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2497 1999 3.28 %
Rwork0.2128 59026 -
obs0.214 61025 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 1.61→78.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 20 402 3842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013469
X-RAY DIFFRACTIONf_angle_d1.02954698
X-RAY DIFFRACTIONf_chiral_restr0.0451558
X-RAY DIFFRACTIONf_plane_restr0.0072612
X-RAY DIFFRACTIONf_dihedral_angle_d4.2546465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.5877700.49492070X-RAY DIFFRACTION48.18
1.65-1.70.35481450.35014272X-RAY DIFFRACTION98.88
1.7-1.750.35611440.29644232X-RAY DIFFRACTION98.29
1.75-1.810.33311440.26584272X-RAY DIFFRACTION98.84
1.81-1.870.2781460.24514305X-RAY DIFFRACTION99.37
1.87-1.950.28831450.23724285X-RAY DIFFRACTION98.91
1.95-2.030.24671460.2424320X-RAY DIFFRACTION99.09
2.03-2.140.30511480.24824340X-RAY DIFFRACTION100
2.14-2.280.25171470.19474376X-RAY DIFFRACTION99.98
2.28-2.450.2081500.18874402X-RAY DIFFRACTION100
2.45-2.70.24621490.20054408X-RAY DIFFRACTION100
2.7-3.090.20811510.19024448X-RAY DIFFRACTION100
3.09-3.890.21851530.18144517X-RAY DIFFRACTION100
3.89-78.390.26371610.2234779X-RAY DIFFRACTION99.8

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