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- PDB-7b25: DtxR-like iron-dependent regulator IdeR (Q43A variant) complexed ... -

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Basic information

Entry
Database: PDB / ID: 7b25
TitleDtxR-like iron-dependent regulator IdeR (Q43A variant) complexed with cobalt and its consensus DNA-binding sequence
Components
  • (consensus DNA-binding sequence) x 2
  • DtxR family iron (Metal) dependent repressor
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / REPRESSOR / REGULATOR / TRANSCRIPTION REGULATOR / METAL SENSOR / IDER / IRON-DEPENDENT REGULATOR / DTXR / HELIX-TURN-HELIX / METAL ION / METAL-BINDING PROTEIN / DNA BINDING / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
FeoA domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily ...FeoA domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Transcriptional repressor, C-terminal / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DtxR family iron (Metal) dependent repressor
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMaurer, D. / Marcos-Torres, F.J. / Griese, J.J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2016-03770 Sweden
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.
Authors: Marcos-Torres, F.J. / Maurer, D. / Juniar, L. / Griese, J.J.
#1: Journal: Biorxiv / Year: 2021
Title: The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Authors: Marcos-Torres, F.J. / Maurer, D. / Griese, J.J.
History
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 31, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / ndb_struct_na_base_pair ...atom_site / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conf / struct_conn / struct_sheet_range
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening ..._ndb_struct_na_base_pair.buckle / _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 / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_work / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Polymer geometry
Details: The model was further rebuilt and refined to improve its geometry, in particular the Rama Z-score. This model has a higher percentage of Ramachandran favored residues and favored rotamers ...Details: The model was further rebuilt and refined to improve its geometry, in particular the Rama Z-score. This model has a higher percentage of Ramachandran favored residues and favored rotamers than the previous model, no Ramachandran or rotamer outliers, and a better Rama Z-score.
Provider: author / Type: Coordinate replacement
Revision 3.0Jul 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 3.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.2Oct 6, 2021Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DtxR family iron (Metal) dependent repressor
B: DtxR family iron (Metal) dependent repressor
C: DtxR family iron (Metal) dependent repressor
D: DtxR family iron (Metal) dependent repressor
E: consensus DNA-binding sequence
F: consensus DNA-binding sequence
aa: DtxR family iron (Metal) dependent repressor
dd: DtxR family iron (Metal) dependent repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,82316
Polymers171,3518
Non-polymers4718
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-191 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.656, 110.856, 86.752
Angle α, β, γ (deg.)90.000, 116.850, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DtxR family iron (Metal) dependent repressor


Mass: 25587.316 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been ...Details: There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been named chains dd and aa. The swap is only possible for chains A and D, but not for chains B and C, due to crystal packing interactions.
Source: (gene. exp.) Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338) (bacteria)
Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338
Gene: A8924_2181 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A9J1W2
#2: DNA chain consensus DNA-binding sequence


Mass: 8893.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others) / References: UniProt: A0A2A9J1W2*PLUS
#3: DNA chain consensus DNA-binding sequence


Mass: 8933.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O / References: UniProt: A0A2A9J1W2*PLUS
Compound detailsThere is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D ...There is a domain swap with symmetry mates. The C-terminal domains associated with chains A and D originate from chains D and A of a symmetry mate, respectively, and have therefore been named chains dd and aa. The swap is only possible for chains A and D, but not for chains B and C, due to crystal packing interactions.
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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 29%(w/v) PEG 3350, 0.28 M ammonium sulfate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.34→93.16 Å / Num. obs: 36928 / % possible obs: 89.5 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Net I/σ(I): 9.1
Reflection shellResolution: 2.34→2.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1847 / CC1/2: 0.599 / Rpim(I) all: 0.511 / Rrim(I) all: 1.323 / % possible all: 61.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B1V

7b1v


Resolution: 2.34→93.16 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.716 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.576 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 1869 5.1 %RANDOM
Rwork0.2673 ---
obs0.268 35059 53.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.74 Å2 / Biso mean: 62.742 Å2 / Biso min: 21.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.27 Å2
2--0.78 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 2.34→93.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7016 1189 8 43 8256
Biso mean--46.78 39.17 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177720
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.56211675
X-RAY DIFFRACTIONr_angle_other_deg1.1131.70517790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1635904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.96520.761394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.649151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4531580
X-RAY DIFFRACTIONr_chiral_restr0.0410.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021776
LS refinement shellResolution: 2.341→2.402 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.277 60 -
obs--1.18 %

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