SAXSdb — 1b1b

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

PROTEIN (IRON DEPENDENT REGULATOR)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–140	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

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 1B1B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–230（230 aa） Chain B 1–230（230 aa）	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
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–230（230 aa） Chain D 1–230（230 aa）	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
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	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	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
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	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	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
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	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	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
1U8R Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions Deposited 2004-08-06	Different construct Different mutation/modification 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 construct Different mutation/modification 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 oligomeric state 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 mutation/modification 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 mutation/modification 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 10 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 1–140； UniProt 1–140

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b1b
Deposition date deposition_date	1998-11-19
Structure title title	IRON DEPENDENT REGULATOR
Keywords keywords	IDER, IRON DEPEDENT REGULATOR, MYCOBACTERIUM TUBERCULOSIS, METAL BINDING PROTEIN; METAL BINDING 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	15.78 Å
Radius of gyration Rg (electron density) rg_electron	15.02 Å
Forward intensity I(0) i0	5007540.00
Molecular weight molecular_weight	15459.0 kDa
Excluded volume excluded_volume	19064 Å³
Envelope volume envelope_volume	21127 Å³
Hydration-shell volume shell_volume	12230 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	20.38 Å
Envelope Rg envelope_rg	15.29 Å
Shape Rg shape_rg	15.06 Å
Total Rg total_rg	15.87 Å
Total atoms total_atoms	1307
Residues n_residues	140
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	51.7 Å
Rg (real space) rg_real	15.76 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	5.0080e+06
I(0) uncertainty (real space) i0_real_error	5.8790e+04
Rg (reciprocal space) rg_reciprocal	15.76 Å
I(0) (reciprocal space) i0_reciprocal	5008000.0000
Solution quality estimate total_estimate	0.8849
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	850700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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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	PROTEIN (IRON DEPENDENT REGULATOR)
Molecular weight formula_weight	15902.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1571

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGV

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b1ba1
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	d1b1ba2
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

CATH v4.4 (2 domains)

Domain ID domain_id	1b1bA01
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	1b1bA02
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

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8. Citations (1)

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Unit-cell length a length_a	92.600 Å
Unit-cell length b length_b	92.600 Å
Unit-cell length c length_c	63.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2800
R_work r_work	0.2800
R_free r_free	0.3600

fit	/app/data/saxs_computation/b1/1b1b/1b1b.fit
pddf	/app/data/pr_computation/b1/1b1b/1b1b.pr.out
profile	/app/data/saxs_computation/b1/1b1b/1b1b.dat

IRON DEPENDENT REGULATOR

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

PROTEIN (IRON DEPENDENT REGULATOR)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction