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- PDB-8q2m: 18mer DNA mimic Foldamer with an Aliphatic linker in complex with... -

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Basic information

Entry
Database: PDB / ID: 8q2m
Title18mer DNA mimic Foldamer with an Aliphatic linker in complex with Sac7d V26A/M29A protein
Components
  • DNA mimic Foldamer
  • DNA-binding protein 7b
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 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 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 Alphatic linker in complex with Sac7d wild protein.
Authors: Deepak, D. / Corvaglia, V. / Wu, J. / Huc, I.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
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_main_chain_plane / 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 7b
A: DNA mimic Foldamer
B: DNA mimic Foldamer


Theoretical massNumber of molelcules
Total (without water)12,6123
Polymers12,6123
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint4 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.920, 70.920, 119.290
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
11A-101-

GOA

21B-111-

GOA

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_0064
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13123
#2: Protein/peptide DNA mimic Foldamer


Mass: 2536.719 Da / Num. of mol.: 2 / 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: 5.74 Å3/Da / Density % sol: 78.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 9 % 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.21→30.71 Å / Num. obs: 3226 / % possible obs: 99.54 % / Redundancy: 37.1 % / Biso Wilson estimate: 115.53 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 23.56
Reflection shellResolution: 3.21→3.32 Å / Redundancy: 39.9 % / Mean I/σ(I) obs: 3.51 / Num. unique obs: 310 / CC1/2: 0.952 / CC star: 0.988 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→30.71 Å / SU ML: 0.3663 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 41.8877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3345 322 10 %
Rwork0.3249 2898 -
obs0.326 3220 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.42 Å2
Refinement stepCycle: LAST / Resolution: 3.21→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 346 0 820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0256853
X-RAY DIFFRACTIONf_angle_d4.1231197
X-RAY DIFFRACTIONf_chiral_restr0.280488
X-RAY DIFFRACTIONf_plane_restr0.0254120
X-RAY DIFFRACTIONf_dihedral_angle_d13.7308181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-4.040.40721540.35991389X-RAY DIFFRACTION99.61
4.05-30.710.31771680.31721509X-RAY DIFFRACTION99.94
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)
10.0999663758486-0.342995455806-0.328985014113.482723196150.443949279351.25795000739-0.6948963988680.363913521985-0.4609900875290.8330167597460.5796554657161.70858262627-0.183266635758-0.496528959117-0.09329582425531.054378630.198241683723-0.2276039544841.37508881254-0.2066446730020.433831009138-9.02481071718-18.08737985164.84833842633
20.708827228729-0.663436723525-0.8936413050653.04191284804-0.2536427629881.596492665960.158027542216-0.289438478514-0.0135413918344-0.480887405160.200524788588-1.0670192961.02945022046-0.9987874028710.2592409030270.5209741728550.0672441135293-0.08084633038521.52885300551-0.06278357835030.785957119723-7.35411988024-17.20175752386.43711309531
31.899412756450.561697086030.2191229730940.2969518030440.2109797299490.18750790308-0.08168873053960.1427385489631.4969246619-0.2265281964120.771611573021.74618367076-0.466815449863-1.04312171163-0.01925380529431.070198912640.02681198715680.04842901756071.159885391350.9782938481531.67238399669-9.44526313087-4.735310077234.44172705742
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 'AA' and (resid 1 through 36 )1 - 361 - 36
22chain 'AA' and (resid 37 through 51 )37 - 5137 - 51
33chain 'AA' and (resid 52 through 63 )52 - 6352 - 63

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