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- PDB-7b1v: DtxR-like iron-dependent regulator IdeR complexed with cobalt -

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Basic information

Entry
Database: PDB / ID: 7b1v
TitleDtxR-like iron-dependent regulator IdeR complexed with cobalt
ComponentsDtxR 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
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / 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
: / DtxR family iron (Metal) dependent repressor
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 25, 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 / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / 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
Item: _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num ..._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_prop.value / _pdbx_struct_conn_angle.ptnr1_label_atom_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 / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _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_free / _refine_ls_shell.R_factor_R_work / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_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, and a good Rama Z-score.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 2.2Oct 6, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / diffrn_source / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _diffrn_source.pdbx_synchrotron_site

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5886
Polymers51,3532
Non-polymers2364
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-38 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.888, 45.564, 66.275
Angle α, β, γ (deg.)109.120, 93.200, 113.980
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25676.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25%(w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→61.1 Å / Num. obs: 17216 / % possible obs: 83.5 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 10.3
Reflection shellResolution: 2.04→2.22 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 862 / CC1/2: 0.658 / Rpim(I) all: 0.465 / Rrim(I) all: 0.748 / % possible all: 54.2

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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: 1U8R

1u8r


Resolution: 2.04→61.1 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.051 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.677 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 838 4.9 %RANDOM
Rwork0.232 ---
obs0.2335 16378 62.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.01 Å2 / Biso mean: 35.79 Å2 / Biso min: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.17 Å2-0.06 Å2
2--0.23 Å20 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 2.04→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 4 67 3491
Biso mean--21.31 30.73 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173448
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.6464681
X-RAY DIFFRACTIONr_angle_other_deg1.0171.5827921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7365436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.29920.876194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66915632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2781539
X-RAY DIFFRACTIONr_chiral_restr0.0330.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
LS refinement shellResolution: 2.043→2.096 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 12 -
Rwork0.35 119 -
all-131 -
obs--6.39 %

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