SAXSdb — 2isy

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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 1–140 Chain B； UniProt 1–140	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

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 2ISY	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
1FX7 CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS Deposited 2000-09-25	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 1–230（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 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
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 Author chain B； 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	2isy
Deposition date deposition_date	2006-10-18
Structure title title	Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR)
Keywords keywords	DNA-binding protein, TRANSCRIPTION; TRANSCRIPTION
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	21.91 Å
Radius of gyration Rg (electron density) rg_electron	21.18 Å
Forward intensity I(0) i0	20602900.00
Molecular weight molecular_weight	33156.0 kDa
Excluded volume excluded_volume	40965 Å³
Envelope volume envelope_volume	50519 Å³
Hydration-shell volume shell_volume	20127 Å³
Envelope diameter envelope_diameter	81.9 Å
Shell Rg shell_rg	27.58 Å
Envelope Rg envelope_rg	22.00 Å
Shape Rg shape_rg	21.27 Å
Total Rg total_rg	21.75 Å
Total atoms total_atoms	2314
Residues n_residues	292
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	81.6 Å
Rg (real space) rg_real	21.92 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	2.0600e+07
I(0) uncertainty (real space) i0_real_error	2.8330e+05
Rg (reciprocal space) rg_reciprocal	21.92 Å
I(0) (reciprocal space) i0_reciprocal	20600000.0000
Solution quality estimate total_estimate	0.8235
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.145
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4734000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.780; Smooth: 0.993

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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	17871.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2521

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASENLYFQGGGHHHHHH

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2isya1
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	d2isya2
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	d2isya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2isyb1
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	d2isyb2
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	d2isyb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2isyA01
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	2isyB01
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

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8. Citations (1)

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Unit-cell length a length_a	41.954 Å
Unit-cell length b length_b	44.743 Å
Unit-cell length c length_c	49.641 Å
Unit-cell angle α angle_alpha	110.18 °
Unit-cell angle β angle_beta	96.57 °
Unit-cell angle γ angle_gamma	108.29 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.955 Å
Low-resolution limit resolution_low	45.130 Å
R factor r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2110

fit	/app/data/saxs_computation/is/2isy/2isy.fit
pddf	/app/data/pr_computation/is/2isy/2isy.pr.out
profile	/app/data/saxs_computation/is/2isy/2isy.dat

Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR)

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

Iron-dependent repressor ideR

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