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- PDB-2isy: Crystal structure of the nickel-activated two-domain iron-depende... -

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Basic information

Entry
Database: PDB / ID: 2isy
TitleCrystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR)
ComponentsIron-dependent repressor ideR
KeywordsTRANSCRIPTION / DNA-binding protein
Function / homology
Function and homology information


catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity ...catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity / iron ion binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / 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 ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsWisedchaisri, G. / Chou, C.J. / Wu, M. / Roach, C. / Rice, A.E. / Holmes, R.K. / Beeson, C. / Hol, W.G.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis
Authors: Wisedchaisri, G. / Chou, C.J. / Wu, M. / Roach, C. / Rice, A.E. / Holmes, R.K. / Beeson, C. / Hol, W.G.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-dependent repressor ideR
B: Iron-dependent repressor ideR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1678
Polymers35,7432
Non-polymers4256
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-54 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.954, 44.743, 49.641
Angle α, β, γ (deg.)110.180, 96.570, 108.290
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains a biological dimer

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Components

#1: Protein Iron-dependent repressor ideR


Mass: 17871.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: IdeR,dtxR / Plasmid: pAER36 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A672, UniProt: P9WMH1*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.6 M Na/K phosphate pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorDetector: CCD / Date: Dec 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 12.6 / Number: 36720 / Rmerge(I) obs: 0.06 / Χ2: 1.05 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 20610 / % possible obs: 91.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.25094.710.0451.036
3.334.297.810.051.079
2.913.339810.0561.056
2.652.9197.610.071.071
2.462.6597.210.0751.04
2.312.4696.810.0891.045
2.22.3196.210.1111.04
2.12.294.710.1251.045
2.022.186.510.151.067
1.952.0258.110.1731.034
ReflectionResolution: 1.95→50 Å / Num. obs: 20610 / % possible obs: 91.8 % / Rmerge(I) obs: 0.06 / Χ2: 1.052 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.020.17312931.03458.1
2.02-2.10.1519511.06786.5
2.1-2.20.12521441.04594.7
2.2-2.310.11121241.0496.2
2.31-2.460.08922031.04596.8
2.46-2.650.07521701.0497.2
2.65-2.910.0721921.07197.6
2.91-3.330.05622001.05698
3.33-4.20.0522081.07997.8
4.2-500.04521251.03694.7

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Phasing

Phasing MRRfactor: 0.414 / Cor.coef. Fo:Fc: 0.574
Highest resolutionLowest resolution
Rotation3 Å25.88 Å
Translation3 Å25.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FX7

1fx7


Resolution: 1.955→45.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.753 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1058 5.1 %RANDOM
Rwork0.176 ---
obs0.178 20606 91.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.607 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20.1 Å2-0.6 Å2
2---1.04 Å2-1.29 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.955→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 14 148 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212416
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.993296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5123.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6831527
X-RAY DIFFRACTIONr_chiral_restr0.0970.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021831
X-RAY DIFFRACTIONr_nbd_refined0.2340.31220
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5291
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.011
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.518
X-RAY DIFFRACTIONr_mcbond_it1.69531529
X-RAY DIFFRACTIONr_mcangle_it2.62942429
X-RAY DIFFRACTIONr_scbond_it2.6514968
X-RAY DIFFRACTIONr_scangle_it3.6885857
LS refinement shellResolution: 1.955→2.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 40 -
Rwork0.224 820 -
obs-860 51.84 %

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