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- PDB-1b1b: IRON DEPENDENT REGULATOR -

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Basic information

Entry
Database: PDB / ID: 1b1b
TitleIRON DEPENDENT REGULATOR
ComponentsPROTEIN (IRON DEPENDENT REGULATOR)
KeywordsMETAL BINDING PROTEIN / IDER / IRON DEPEDENT REGULATOR / MYCOBACTERIUM TUBERCULOSIS
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 / 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 ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / FeoA domain / 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 / 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
Iron-dependent repressor IdeR / Iron-dependent repressor IdeR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPohl, E. / Holmes, R.K. / Hol, W.G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied.
Authors: Pohl, E. / Holmes, R.K. / Hol, W.G.
History
DepositionNov 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IRON DEPENDENT REGULATOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1294
Polymers15,9021
Non-polymers2273
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.600, 92.600, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein PROTEIN (IRON DEPENDENT REGULATOR) / IDER


Mass: 15902.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PMTBKS / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P0A672, UniProt: P9WMH1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.92 Å3/Da / Density % sol: 74.98 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 2:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
310 mMzinc acetate1reservoir
410 mMTris-HCl1reservoir
510 %(w/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 9277 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Rsym value: 0.07 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 10 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.45 / % possible all: 93
Reflection
*PLUS
Num. measured all: 147166 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMORE

Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.36 927 10 %RANDOM
Rwork0.28 ---
obs0.28 9277 95 %-
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 7 264 1571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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