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- PDB-7bcb: Crystal structure of the HTH DNA binding protein ArdK from R388 p... -

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Basic information

Entry
Database: PDB / ID: 7bcb
TitleCrystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to IR3 DNA
Components
  • DNA (5'-D(*TP*AP*AP*TP*GP*TP*CP*AP*AP*AP*TP*AP*TP*TP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*TP*TP*TP*GP*AP*CP*AP*TP*TP*A)-3')
  • KORA domain-containing protein
KeywordsDNA BINDING PROTEIN / Helix Turn Helix / Direct repeat / Plasmid conjugation
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2690 / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / : / RNA polymerase sigma factor, region 3/4-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / TrfB transcriptional repressor protein domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFernandez-Lopez, R. / Boer, D.R. / Moncalian, G.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55534-C2-2-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-093885-B-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.
Authors: Fernandez-Lopez, R. / Ruiz, R. / Del Campo, I. / Gonzalez-Montes, L. / Boer, D.R. / de la Cruz, F. / Moncalian, G.
History
DepositionDec 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_ref_seq_dif / symmetry
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 / _cell.volume / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.version / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq_dif.details / _symmetry.space_group_name_Hall
Description: Chirality error / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KORA domain-containing protein
B: KORA domain-containing protein
C: DNA (5'-D(*TP*AP*AP*TP*GP*TP*CP*AP*AP*AP*TP*AP*TP*TP*GP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*TP*TP*TP*GP*AP*CP*AP*TP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,0634
Polymers36,0634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-52 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.890, 77.220, 114.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein KORA domain-containing protein


Mass: 12518.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pET29c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I6B7
#2: DNA chain DNA (5'-D(*TP*AP*AP*TP*GP*TP*CP*AP*AP*AP*TP*AP*TP*TP*GP*AP*CP*A)-3')


Mass: 5522.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*TP*TP*TP*GP*AP*CP*AP*TP*TP*A)-3')


Mass: 5504.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% 10,000 polyethylene glycol, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→77.22 Å / Num. obs: 12277 / % possible obs: 98.3 % / Redundancy: 8.1 % / Biso Wilson estimate: 61.38 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.102 / Net I/σ(I): 4.6
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1744 / CC1/2: 0.94 / Rrim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.25data extraction
SCALACCP4 7.0.078data scaling
PHENIX1.17.1_3660phasing
MOSFLM7.2.2data reduction
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BCA

7bca


Resolution: 2.8→45.89 Å / SU ML: 0.504 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.7723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2983 465 4.78 %
Rwork0.2529 9273 -
obs0.2551 9738 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 731 0 0 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592335
X-RAY DIFFRACTIONf_angle_d0.77993306
X-RAY DIFFRACTIONf_chiral_restr0.0404376
X-RAY DIFFRACTIONf_plane_restr0.008308
X-RAY DIFFRACTIONf_dihedral_angle_d25.4014563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.46831470.36542970X-RAY DIFFRACTION94.89
3.21-4.040.30211570.26843039X-RAY DIFFRACTION96.27
4.04-45.890.25581610.21853264X-RAY DIFFRACTION98.7

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