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- PDB-1fx7: CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYC... -

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Basic information

Entry
Database: PDB / ID: 1fx7
TitleCRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsIRON-DEPENDENT REPRESSOR IDER
KeywordsSIGNALING PROTEIN / IdeR / DtxR / iron-dependent 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 / 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
: / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsFeese, M.D. / Ingason, B.P. / Goranson-Siekierke, J. / Holmes, R.K. / Hol, W.J.G.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the iron-dependent regulator from Mycobacterium tuberculosis at 2.0-A resolution reveals the Src homology domain 3-like fold and metal binding function of the third domain.
Authors: Feese, M.D. / Ingason, B.P. / Goranson-Siekierke, J. / Holmes, R.K. / Hol, W.G.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: 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_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_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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: 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)103,52734
Polymers101,1274
Non-polymers2,39930
Water14,268792
1
A: IRON-DEPENDENT REPRESSOR IDER
B: IRON-DEPENDENT REPRESSOR IDER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,97419
Polymers50,5642
Non-polymers1,41017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-207 kcal/mol
Surface area20590 Å2
MethodPISA
2
C: IRON-DEPENDENT REPRESSOR IDER
D: IRON-DEPENDENT REPRESSOR IDER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,55315
Polymers50,5642
Non-polymers98913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-116 kcal/mol
Surface area19320 Å2
MethodPISA
3
A: IRON-DEPENDENT REPRESSOR IDER
B: IRON-DEPENDENT REPRESSOR IDER
hetero molecules

C: IRON-DEPENDENT REPRESSOR IDER
D: IRON-DEPENDENT REPRESSOR IDER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52734
Polymers101,1274
Non-polymers2,39930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area8920 Å2
ΔGint-340 kcal/mol
Surface area38610 Å2
MethodPISA
4
A: IRON-DEPENDENT REPRESSOR IDER
B: IRON-DEPENDENT REPRESSOR IDER
hetero molecules

C: IRON-DEPENDENT REPRESSOR IDER
D: IRON-DEPENDENT REPRESSOR IDER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52734
Polymers101,1274
Non-polymers2,39930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
Buried area8600 Å2
ΔGint-334 kcal/mol
Surface area38930 Å2
MethodPISA
5
A: IRON-DEPENDENT REPRESSOR IDER
hetero molecules

C: IRON-DEPENDENT REPRESSOR IDER
hetero molecules

D: IRON-DEPENDENT REPRESSOR IDER
hetero molecules

B: IRON-DEPENDENT REPRESSOR IDER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52734
Polymers101,1274
Non-polymers2,39930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area8000 Å2
ΔGint-328 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.309, 113.970, 236.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains two functional dimers that comprise chains A & B, and chains C & D.

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Components

#1: Protein
IRON-DEPENDENT REPRESSOR IDER


Mass: 25281.846 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PBLUESCRIPT KS / Organelle (production host): TB444 COSMID / Production host: Escherichia coli (E. coli) / References: UniProt: P0A672, UniProt: P9WMH1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0 M lithium sulfate 0.01 M magnesium chloride 0.1 M MES buffer ~0.1 mM 21 bp duplex DNA oligomer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-10 mg/mlprotein11
250 mM12NaCl
310 mMTris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: APS-1 / Detector: CCD / Date: Dec 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 82283 / Num. obs: 82283 / % possible obs: 95.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.311 / Num. unique all: 3171 / % possible all: 75.4
Reflection
*PLUS
Num. measured all: 896284
Reflection shell
*PLUS
% possible obs: 75.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
DMmodel building
REFMACrefinement
TNTrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
DMphasing
RefinementResolution: 2→20 Å / SU ML: 0.12 / Stereochemistry target values: Engh & Huber
Details: restrained Maximum Likelihood by Conjugate Direction in Refmac with anisotropic overall B factors, isotropic individual B factors, and Moews & Krezinger (J Mol Biol. 1975 Jan 15;91(2):229-32) ...Details: restrained Maximum Likelihood by Conjugate Direction in Refmac with anisotropic overall B factors, isotropic individual B factors, and Moews & Krezinger (J Mol Biol. 1975 Jan 15;91(2):229-32) type bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5 -5% of reflections reserved using the UNIQUEIFY script from CCP4
Rwork0.214 ---
all-82283 --
obs-82283 95.6 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 98 792 7817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_deg1.6
X-RAY DIFFRACTIONp_planar_tor2.6
X-RAY DIFFRACTIONp_staggered_tor16.7
X-RAY DIFFRACTIONp_transverse_tor26.6
X-RAY DIFFRACTIONp_planar_d0.016
X-RAY DIFFRACTIONp_mcbond_it5.7
X-RAY DIFFRACTIONp_scbond_it6.7
Software
*PLUS
Name: 'REFMAC AND TNT5E' / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 5 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_planar_d
X-RAY DIFFRACTIONt_mcbond_it5.7
X-RAY DIFFRACTIONt_scbond_it6.7
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.04 Å / Rfactor Rfree: 0.316 / Num. reflection obs: 3201 / Rfactor obs: 0.24

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