1fx7

CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS

Method: X-RAY DIFFRACTION D_max: 133.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

IRON-DEPENDENT REPRESSOR IDER

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230	Not recorded	SO4 SULFATE ION × 11 CO COBALT (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；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	Resolution 2.00 Å R-free 0.272
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–230 Chain D； UniProt 1–230	Not recorded	SO4 SULFATE ION × 6 CO COBALT (II) ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；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	Resolution 2.00 Å R-free 0.272
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230	Not recorded	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；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	Resolution 2.00 Å R-free 0.272
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230	Not recorded	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；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	Resolution 2.00 Å R-free 0.272
5	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230	Not recorded	SO4 SULFATE ION × 17 CO COBALT (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；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	Resolution 2.00 Å R-free 0.272

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1FX7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B1B IRON DEPENDENT REGULATOR Deposited 1998-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–140（140 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.60 Å R-free 0.360
1U8R Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions Deposited 2004-08-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–230（230 aa） Chain B 1–230（230 aa） Chain C 1–230（230 aa） Chain D 1–230（230 aa）	Not recorded	CO COBALT (II) ION × 12 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；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	Resolution 2.75 Å R-free 0.265
1U8R Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions Deposited 2004-08-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain G 1–230（230 aa） Chain H 1–230（230 aa） Chain I 1–230（230 aa） Chain J 1–230（230 aa）	Not recorded	CO COBALT (II) ION × 12 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；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	Resolution 2.75 Å R-free 0.265
2ISY Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR) Deposited 2006-10-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–140（140 aa） Chain B 1–140（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；0.6 M Na/K phosphate pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.96 Å R-free 0.211
2ISZ Crystal structure of a two-domain IdeR-DNA complex crystal form I Deposited 2006-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–140（140 aa） Chain B 1–140（140 aa） Chain C 1–140（140 aa） Chain D 1–140（140 aa）	Not recorded	NI NICKEL (II) ION × 12 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.239
2IT0 Crystal structure of a two-domain IdeR-DNA complex crystal form II Deposited 2006-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–140（140 aa） Chain B 1–140（140 aa） Chain C 1–140（140 aa） Chain D 1–140（140 aa）	Not recorded	NI NICKEL (II) ION × 12 ACT ACETATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；26% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris HCl pH 8.5, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.273

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IDER_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 1–230 Author chain B； PDBConstruct 1–230； UniProt 1–230 Author chain C； PDBConstruct 1–230； UniProt 1–230 Author chain D； PDBConstruct 1–230； UniProt 1–230

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1fx7
Deposition date deposition_date	2000-09-25
Structure title title	CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS
Keywords keywords	IdeR, DtxR, iron-dependent regulator, Mycobacterium tuberculosis, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.81 Å
Radius of gyration Rg (electron density) rg_electron	40.22 Å
Forward intensity I(0) i0	166911000.00
Molecular weight molecular_weight	100250.0 kDa
Excluded volume excluded_volume	123710 Å³
Envelope volume envelope_volume	171810 Å³
Hydration-shell volume shell_volume	37293 Å³
Envelope diameter envelope_diameter	136.9 Å
Shell Rg shell_rg	43.50 Å
Envelope Rg envelope_rg	39.51 Å
Shape Rg shape_rg	40.26 Å
Total Rg total_rg	40.29 Å
Total atoms total_atoms	6969
Residues n_residues	890
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	133.4 Å
Rg (real space) rg_real	40.10 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	1.6690e+08
I(0) uncertainty (real space) i0_real_error	3.2220e+06
Rg (reciprocal space) rg_reciprocal	39.93 Å
I(0) (reciprocal space) i0_reciprocal	166900000.0000
Solution quality estimate total_estimate	0.7817
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.746
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11520000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.726; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	IRON-DEPENDENT REPRESSOR IDER
Molecular weight formula_weight	25281.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7817

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI Class编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	792

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1fx7a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1fx7a2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1fx7a3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1fx7b1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1fx7b2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1fx7b3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1fx7c1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1fx7c2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1fx7c3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1fx7d1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1fx7d2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1fx7d3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

CATH v4.4 (12 domains)

Domain ID domain_id	1fx7A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1fx7A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1fx7A03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1fx7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1fx7B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1fx7B03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1fx7C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1fx7C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1fx7C03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1fx7D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1fx7D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1fx7D03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

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8. Citations (1)

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Unit-cell length a length_a	46.309 Å
Unit-cell length b length_b	113.970 Å
Unit-cell length c length_c	236.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2720

fit	/app/data/saxs_computation/fx/1fx7/1fx7.fit
pddf	/app/data/pr_computation/fx/1fx7/1fx7.pr.out
profile	/app/data/saxs_computation/fx/1fx7/1fx7.dat