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- PDB-8cmn: 18mer DNA mimic Foldamer with an aliphatic linker in complex with... -

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Basic information

Entry
Database: PDB / ID: 8cmn
Title18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein
Components
  • DNA-binding protein 7d
  • N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide
KeywordsDNA BINDING PROTEIN / Foldamer / DNA mimic / histone
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 DSM 639 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDeepak, D. / Corvaglia, V. / Wu, J. / Huc, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: 18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein
Authors: Deepak, D. / Corvaglia, V. / Wu, J. / Huc, I.
History
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Category: chem_comp / chem_comp_atom / chem_comp_bond / Item: _chem_comp.type
Revision 1.2Sep 27, 2023Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / struct_conn
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 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: DNA-binding protein 7d
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)12,7003
Polymers12,7003
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.410, 71.410, 116.170
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-

GOA

21C-1-

GOA

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Components

#1: Protein DNA-binding protein 7d / 7 kDa DNA-binding protein d / Sac7d


Mass: 7626.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_0064 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): 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: 2536.719 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.88 Å3/Da / Density % sol: 79.17 %
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: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.65→42.34 Å / Num. obs: 5508 / % possible obs: 99.62 % / Redundancy: 6.9 % / Biso Wilson estimate: 74.99 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 18.81
Reflection shellResolution: 2.65→2.75 Å / Num. unique obs: 531 / CC1/2: 0.81 / CC star: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→42.34 Å / SU ML: 0.445 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.1161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2974 547 9.94 %
Rwork0.2614 4955 -
obs0.2651 5502 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms495 0 346 7 848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078877
X-RAY DIFFRACTIONf_angle_d2.68611230
X-RAY DIFFRACTIONf_chiral_restr0.253189
X-RAY DIFFRACTIONf_plane_restr0.0132122
X-RAY DIFFRACTIONf_dihedral_angle_d13.0023182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.43091300.35851194X-RAY DIFFRACTION99.77
2.92-3.340.34321340.29041205X-RAY DIFFRACTION99.78
3.34-4.20.29121360.2421226X-RAY DIFFRACTION99.56
4.21-42.340.27231470.25311330X-RAY DIFFRACTION99.53
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)
1-0.0424056302552-0.2059872222380.246529559024-0.1104220822880.0469550260810.05877203750180.9569099128161.198182249-0.7806404861580.001440184546520.7999826186861.856708081261.166547156171.3308704038-5.17438182501E-60.5586438116930.0126414678229-0.04963813153610.569484637222-0.1740907237890.342914358816-5.42331665203-20.14043292412.28437364025
20.3045520872880.0912578012191-0.08960271329250.0146525221496-0.08464764746320.01533915456540.3839095356350.620420165336-0.459753728102-1.17707534916-0.1235272792580.032788842520.88496394343-0.807948074851-3.224496567E-70.645831996952-0.00346075580414-0.02304735777620.683393722336-0.1113424889990.689142976971-8.94627918238-20.38023208840.465146021811
30.3620265552960.101960621882-0.3140240875060.445873493271-0.3527017094340.540773137119-0.353126908008-0.409249929859-0.716930647327-0.1316287207530.615533016753-0.0647135103956-0.844503067902-0.4550801166572.0743353958E-70.4012997728360.05124605563730.04432848763650.378192899319-0.02278048852950.422222899283-10.7589106924-13.83849028119.21116909842
40.02804117377480.10249316997-0.8927640444350.2079261729890.1720085700181.148261974210.611042794006-0.01762053728050.186565522787-0.1223919247-0.2498803033620.206892617699-0.1243514399130.12114665945-2.83697467139E-70.4651316302030.05450178281370.1166038798960.3190931850220.05911010743020.410890728621-8.59808970831-10.11935170525.63823093927
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )1 - 101 - 10
22chain 'A' and (resid 11 through 19 )11 - 1911 - 19
33chain 'A' and (resid 20 through 36 )20 - 3620 - 36
44chain 'A' and (resid 37 through 63 )37 - 6337 - 63

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