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Basic information

Entry
Database: PDB / ID: 1u8r
TitleCrystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions
Components
  • Iron-dependent repressor ideR
  • mbtA operator DNA
  • mbtB operator DNA
Keywordsmetal-binding protein / Transcription/DNA / IdeR / iron-dependent regulator / iron acquisition / siderophores / Mycobacterium tuberculosis / Transcription-DNA COMPLEX
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 transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / FeoA domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation 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 / Diphtheria Toxin Repressor; domain 2 / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWisedchaisri, G. / Holmes, R.K. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions.
Authors: Wisedchaisri, G. / Holmes, R.K. / Hol, W.G.J.
History
DepositionAug 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states that Asp 136 appears to be more correct than Val136 according to the ...SEQUENCE Author states that Asp 136 appears to be more correct than Val136 according to the residue's chemical environment. This is also consistent with a previously submitted PDB 1FX7. The mutation might have occurred in the plasmid.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: mbtA operator DNA
F: mbtB operator DNA
K: mbtA operator DNA
L: mbtB operator DNA
A: Iron-dependent repressor ideR
B: Iron-dependent repressor ideR
C: Iron-dependent repressor ideR
D: Iron-dependent repressor ideR
G: Iron-dependent repressor ideR
H: Iron-dependent repressor ideR
I: Iron-dependent repressor ideR
J: Iron-dependent repressor ideR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,45544
Polymers242,85712
Non-polymers1,59832
Water91951
1
E: mbtA operator DNA
F: mbtB operator DNA
A: Iron-dependent repressor ideR
B: Iron-dependent repressor ideR
C: Iron-dependent repressor ideR
D: Iron-dependent repressor ideR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,22822
Polymers121,4286
Non-polymers79916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: mbtA operator DNA
L: mbtB operator DNA
G: Iron-dependent repressor ideR
H: Iron-dependent repressor ideR
I: Iron-dependent repressor ideR
J: Iron-dependent repressor ideR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,22822
Polymers121,4286
Non-polymers79916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.959, 107.959, 215.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe asymmetric unit contains two biological assemblies. Assembly 1 contains IdeR molecule A, B, C, and D, and DNA molecules E and F. / The asymmetric unit contains two biological assemblies. Assembly 1 contains IdeR molecule G, H, I, and J, and DNA molecules K and L.

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Components

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DNA chain , 2 types, 4 molecules EKFL

#1: DNA chain mbtA operator DNA


Mass: 10112.492 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain mbtB operator DNA


Mass: 10188.573 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 8 molecules ABCDGHIJ

#3: Protein
Iron-dependent repressor ideR


Mass: 25281.846 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ideR, dtxR / Plasmid: PBLUESCRIPT II KS (+--) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A672, UniProt: P9WMH1*PLUS

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Non-polymers , 3 types, 83 molecules

#4: Chemical...
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Co
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7% w/v PEG 8000, 0.2 M calcium acetate, 0.1 M imidazole, 0.01 M cobalt chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
3imidazol11
4cobalt chloride11
5H2O11
6PEG 800012
7calcium acetate12
8cobalt chloride12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 72867 / Num. obs: 63753 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.04 % / Biso Wilson estimate: 52.1 Å2 / Rsym value: 0.81 / Net I/σ(I): 10.87
Reflection shellResolution: 2.75→2.85 Å / Mean I/σ(I) obs: 2.09 / Num. unique all: 4866 / Rsym value: 0.434 / % possible all: 65.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FX7 and 1DDN

1fx7

1ddn


Resolution: 2.75→46.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2515021.19 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3193 5.1 %RANDOM
Rwork0.23 ---
all0.232 72867 --
obs0.232 63213 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0626 Å2 / ksol: 0.312897 e/Å3
Displacement parametersBiso mean: 84.9 Å2
Baniso -1Baniso -2Baniso -3
1--27.39 Å2-5.28 Å20 Å2
2---27.39 Å20 Å2
3---54.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a1.17 Å1.18 Å
Refinement stepCycle: LAST / Resolution: 2.75→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13704 2694 32 51 16481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.564 432 5.3 %
Rwork0.543 7766 -
obs--67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM

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