SAXSdb — 8cyf

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

Redox- and pH-responsive transcriptional regulator WhiB3

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	Insufficient information Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–102	Not recorded	RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta × 1 （A0A654TMB9,A1KGE7） ;DNA (5'-D(GPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(CPAPCPCPAPCPAPAPCPCPGPAPTPTPTPT)-3') ; × 1 SF4 IRON/SULFUR CLUSTER × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Ca(Ac)2, 0.1 M Na Cacodylate, pH 6.5, 10%~13% PEG8000	Resolution 2.44 Å R-free 0.251

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 8CYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8CWR Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group R3 Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–90（90 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 SO4 SULFATE ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 NI NICKEL (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；10-20 mM NiCl2, 0.8-1.0 M Li2SO4	Resolution 1.50 Å R-free 0.212
8CWT Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group P43212 Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–90（90 aa） Chain C 1–90（90 aa） Chain E 1–90（90 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3 SO4 SULFATE ION × 25 NI NICKEL (II) ION × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20 mM NiCl2, 0.8-1.0 M Li2SO4	Resolution 1.35 Å R-free 0.174

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

View Construct and Data Evidence

UniProt name	WHIB3_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 1–102

RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis

UniProt A0A654TMB9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 295–377	Not recorded	Redox- and pH-responsive transcriptional regulator WhiB3 × 1 （P9WF41） ;DNA (5'-D(GPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(CPAPCPCPAPCPAPAPCPCPGPAPTPTPTPT)-3') ; × 1 SF4 IRON/SULFUR CLUSTER × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Ca(Ac)2, 0.1 M Na Cacodylate, pH 6.5, 10%~13% PEG8000	Resolution 2.44 Å R-free 0.251

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 8CYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KUF Transcription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA Deposited 2020-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 295–377（83 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.2-0.3 M NH4H2PO4	Resolution 2.60 Å R-free 0.255
7KUG Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera Deposited 2020-11-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–377（83 aa）	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 8；291 K；0.1 M Tris pH 8.0, 10-15% PEG8000, 2-5% PGA	Resolution 1.55 Å R-free 0.200
7KUG Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera Deposited 2020-11-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 295–377（83 aa）	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 8；291 K；0.1 M Tris pH 8.0, 10-15% PEG8000, 2-5% PGA	Resolution 1.55 Å R-free 0.200

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A654TMB9_MYCTX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 9–91； UniProt 295–377

RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis

UniProt A1KGE7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 815–829	Not recorded	Redox- and pH-responsive transcriptional regulator WhiB3 × 1 （P9WF41） ;DNA (5'-D(GPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(CPAPCPCPAPCPAPAPCPCPGPAPTPTPTPT)-3') ; × 1 SF4 IRON/SULFUR CLUSTER × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Ca(Ac)2, 0.1 M Na Cacodylate, pH 6.5, 10%~13% PEG8000	Resolution 2.44 Å R-free 0.251

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 8CYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KUF Transcription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA Deposited 2020-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 815–829（15 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.2-0.3 M NH4H2PO4	Resolution 2.60 Å R-free 0.255
7KUG Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera Deposited 2020-11-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 815–829（15 aa）	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 8；291 K；0.1 M Tris pH 8.0, 10-15% PEG8000, 2-5% PGA	Resolution 1.55 Å R-free 0.200
7KUG Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera Deposited 2020-11-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 815–829（15 aa）	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 8；291 K；0.1 M Tris pH 8.0, 10-15% PEG8000, 2-5% PGA	Resolution 1.55 Å R-free 0.200

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOB_MYCBP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 98–112； UniProt 815–829

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	8cyf
Deposition date deposition_date	2022-05-23
Structure title title	WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA
Keywords keywords	redox sensor, transcriptional factor, protein-DNA complex, TRANSCRIPTION, TRANSCRIPTION-DNA-Transferase complex; TRANSCRIPTION/DNA/Transferase
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	21.42 Å
Radius of gyration Rg (electron density) rg_electron	20.60 Å
Forward intensity I(0) i0	23381100.00
Molecular weight molecular_weight	28951.0 kDa
Excluded volume excluded_volume	32811 Å³
Envelope volume envelope_volume	43727 Å³
Hydration-shell volume shell_volume	18572 Å³
Envelope diameter envelope_diameter	79.5 Å
Shell Rg shell_rg	26.15 Å
Envelope Rg envelope_rg	20.83 Å
Shape Rg shape_rg	20.56 Å
Total Rg total_rg	21.33 Å
Total atoms total_atoms	1971
Residues n_residues	196
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	75.1 Å
Rg (real space) rg_real	21.44 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.3380e+07
I(0) uncertainty (real space) i0_real_error	2.7380e+05
Rg (reciprocal space) rg_reciprocal	21.43 Å
I(0) (reciprocal space) i0_reciprocal	23380000.0000
Solution quality estimate total_estimate	0.6432
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.301
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0507
Highest regularization parameter α highest_alpha	2373000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Redox- and pH-responsive transcriptional regulator WhiB3
Molecular weight formula_weight	11630.3 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	1974

MPQPEQLPGPNADIWNWQLQGLCRGMDSSMFFHPDGERGRARTQREQRAKEMCRRCPVIEACRSHALEVGEPYGVWGGLSESERDLLLKGTMGRTRGIRRTA

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 polymer

Description description	RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	12650.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAHHHHHHVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLDGSSGSGTPEERLLRAIFGEKA

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 3 Entity 3 polymer

Description description	;DNA (5'-D(GPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ;
Molecular weight formula_weight	4993.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAAAATCGGTTGTGGT

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(CPAPCPCPAPCPAPAPCPCPGPAPTPTPTPT)-3') ;
Molecular weight formula_weight	4802.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CACCACAACCGATTTT

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	50.697 Å
Unit-cell length b length_b	72.934 Å
Unit-cell length c length_c	95.380 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	4

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

Resolution resolution	2.440 Å
Low-resolution limit resolution_low	38.150 Å
R factor r_factor	0.2238
R_work r_work	0.2224
R_free r_free	0.2513

fit	/app/data/saxs_computation/cy/8cyf/8cyf.fit
pddf	/app/data/pr_computation/cy/8cyf/8cyf.pr.out
profile	/app/data/saxs_computation/cy/8cyf/8cyf.dat

WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA

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

Redox- and pH-responsive transcriptional regulator WhiB3

State in the Current Structure

Other States of the Same Protein in the Database

RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)