SAXSdb — 5oay

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

Transcriptional regulator WhiB1

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

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 1–84	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 300；Pressure 1 NMR sample composition：25 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 5OAY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ONO Complex structure of WhiB1 and region 4 of SigA in C2221 space group Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.237
6ONO Complex structure of WhiB1 and region 4 of SigA in C2221 space group Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.237
6ONU Complex structure of WhiB1 and region 4 of SigA in P21 space group. Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.235
6ONU Complex structure of WhiB1 and region 4 of SigA in P21 space group. Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.235
6ONU Complex structure of WhiB1 and region 4 of SigA in P21 space group. Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.235
6ONU Complex structure of WhiB1 and region 4 of SigA in P21 space group. Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa） Fragment：UNP residues 1-76	Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350	Resolution 1.85 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	WHIB1_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–94； UniProt 1–84

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	5oay
Deposition date deposition_date	2017-06-25
Structure title title	M. tuberculosis [4Fe-4S] protein WhiB1 is a four-helix bundle that forms a NO-sensitive complex with sigmaA and regulates the major virulence factor ESX-1
Keywords keywords	nitric oxide, sigmaA, iron-sulfur, tuberculosis, Wbl protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.95 Å
Radius of gyration Rg (electron density) rg_electron	12.19 Å
Forward intensity I(0) i0	141389000.00
Molecular weight molecular_weight	87822.0 kDa
Excluded volume excluded_volume	104910 Å³
Envelope volume envelope_volume	17722 Å³
Hydration-shell volume shell_volume	11334 Å³
Envelope diameter envelope_diameter	46.1 Å
Shell Rg shell_rg	19.05 Å
Envelope Rg envelope_rg	13.77 Å
Shape Rg shape_rg	12.29 Å
Total Rg total_rg	12.15 Å
Total atoms total_atoms	11600
Residues n_residues	760
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	44.1 Å
Rg (real space) rg_real	11.96 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.4140e+08
I(0) uncertainty (real space) i0_real_error	1.6230e+06
Rg (reciprocal space) rg_reciprocal	11.96 Å
I(0) (reciprocal space) i0_reciprocal	141400000.0000
Solution quality estimate total_estimate	0.8373
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.4 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.268
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	99120.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Description description	Transcriptional regulator WhiB1
Molecular weight formula_weight	10383.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11600

来源生物 organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI Class编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Mycobacterium smegmatis

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/oa/5oay/5oay.fit
pddf	/app/data/pr_computation/oa/5oay/5oay.pr.out
profile	/app/data/saxs_computation/oa/5oay/5oay.dat

M. tuberculosis [4Fe-4S] protein WhiB1 is a four-helix bundle that forms a NO-sensitive complex with sigmaA and regulates the major virulence factor ESX-1

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

Transcriptional regulator WhiB1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)