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- PDB-8qpc: 18mer DNA mimic Foldamer with an Aromatic linker in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8qpc
Title18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein
Components
  • (N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide) x 2
  • DNA-binding protein 7b
KeywordsDNA BINDING PROTEIN / Foldamer / DNA mimic foldamer / DNA mimicry / Sac7d
Function / homologyDNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / RNA endonuclease activity / DNA binding / cytoplasm / DNA-binding protein 7d
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsDeepak, D. / Corvaglia, V. / Wu, J. / Huc, I.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)325871075 (CRC1309-C7) Germany
European Research Council (ERC)ERC-2021-ADG-320892European Union
Citation
Journal: To Be Published
Title: DNA-Mimic Foldamer Recognition of a Chromosomal Protein
Authors: Deepak, D. / Corvaglia, V. / Wu, J. / Allmendinger, L. / Huc, I.
#4: Journal: Nat Chem / Year: 2018
Title: Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA.
Authors: Ziach, K. / Chollet, C. / Parissi, V. / Prabhakaran, P. / Marchivie, M. / Corvaglia, V. / Bose, P.P. / Laxmi-Reddy, K. / Godde, F. / Schmitter, J.M. / Chaignepain, S. / Pourquier, P. / Huc, I.
#5: Journal: Nucleic Acids Res / Year: 2005
Title: Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
Authors: Chen, C.Y. / Ko, T.P. / Lin, T.W. / Chou, C.C. / Chen, C.J. / Wang, A.H.
History
DepositionOct 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_2
Revision 3.0May 1, 2024Group: Atomic model / Polymer sequence / Category: atom_site / entity_poly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: DNA-binding protein 7b
B: N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide
C: N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide


Theoretical massNumber of molelcules
Total (without water)12,6643
Polymers12,6643
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.907, 70.907, 121.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#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
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11B-1-

DBU

21B-1-

DBU

31C-1-

DBB

41C-1-

DBB

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "C"

NCS oper: (Code: givenMatrix: (-0.714214186265, 0.415209854254, 0.563470383488), (0.43441282378, -0.36825835054, 0.821992266261), (0.548801963074, 0.831857297971, 0.0826428529187)Vector: 6. ...NCS oper: (Code: given
Matrix: (-0.714214186265, 0.415209854254, 0.563470383488), (0.43441282378, -0.36825835054, 0.821992266261), (0.548801963074, 0.831857297971, 0.0826428529187)
Vector: 6.38180757637, -49.5668002147, 33.2015651841)

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Components

#1: Protein DNA-binding protein 7b / 7 kDa DNA-binding protein b / Sac7b


Mass: 7538.743 Da / Num. of mol.: 1 / Mutation: V26A/M29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_0064 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE 3 plys S / References: UniProt: P13123
#2: Protein/peptide N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide


Mass: 2561.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide


Mass: 2563.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 5.87 Å3/Da / Density % sol: 79.05 % / Description: Diamond shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 % PEG 400, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 14, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 3.24→61.41 Å / Num. obs: 2973 / % possible obs: 89.51 % / Redundancy: 17.4 % / Biso Wilson estimate: 91.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.81
Reflection shellResolution: 3.241→3.356 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 244 / CC1/2: 0.938 / % possible all: 81.27

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→61.41 Å / SU ML: 0.0849 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3481 139 4.83 %
Rwork0.3356 2740 -
obs0.3362 2879 89.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.77 Å2
Refinement stepCycle: LAST / Resolution: 3.24→61.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms462 0 350 0 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0277846
X-RAY DIFFRACTIONf_angle_d3.80651198
X-RAY DIFFRACTIONf_chiral_restr0.284788
X-RAY DIFFRACTIONf_plane_restr0.021120
X-RAY DIFFRACTIONf_dihedral_angle_d16.3208181
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.75222926084 Å
LS refinement shellResolution: 3.24→61.41 Å
RfactorNum. reflection% reflection
Rfree0.3481 139 -
Rwork0.3356 2740 -
obs--89.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.426692234259-0.183161309995-0.127890711451.581053105990.3736725008190.1116402205150.211371950410.633482259370.06385064914870.3659322754560.1757639590430.03030587362-0.181527822517-0.4239125784660.4050022229520.2651178894730.5604607713690.618423561082.23948649354-1.074339075041.06396558219-5.99648755697-20.9500944693.2429973661
21.106322173230.4219145024941.198527969263.20107002993-1.257080060722.1505509067-0.4213651090891.23135321830.1562290534080.5907612172081.107214222651.6713842152-0.689125995534-0.1215798244841.213088987050.116270166225-0.20467907913-0.4097022284460.9573116840250.522259961571.69584567022-11.1703507601-17.49226462556.82340166847
31.48483619589-0.591474154642.396015743650.973969041116-1.289153970884.07040713516-0.00436077084440.71618421090.852404527993-0.8423866158641.857707964541.462028853680.08414201389121.042489985851.619655596760.86688455408-0.1169804194540.6740844823770.9907725957160.05988086036331.52863108341-6.78920688884-6.43715360685.37856848064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: AA / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'AA' and (resid 1 through 10 )1 - 101 - 10
22chain 'AA' and (resid 11 through 46 )11 - 4611 - 46
33chain 'AA' and (resid 47 through 63 )47 - 6347 - 63

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