SAXSdb — 7kuf

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

Probable transcriptional regulator WhiB7

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 1–92	Not recorded	RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera × 1 （A0A654TMB9,A1KGE7） ;DNA (5'-D(CPAPGPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(GPAPCPCPAPCPAPAPCPCPGPAPTPTPTPTPCPT)-3') ; × 1 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

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 7KUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KIF Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor Deposited 2020-10-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain Z 1–92（92 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
7KIM Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor Deposited 2020-10-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain Z 1–92（92 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
7KUG Fe-S cluster-bound transcription activator WhiB7 in complex with the SigmaAr4-RNAP Beta flap tip chimera Deposited 2020-11-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–79（79 aa）	Mutation：L27M, L42M 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 construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–79（79 aa）	Mutation：L27M, L42M 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

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	WHB7A_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–92； UniProt 1–92

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

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	Probable transcriptional regulator WhiB7 × 1 （Q6MX01） ;DNA (5'-D(CPAPGPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(GPAPCPCPAPCPAPAPCPCPGPAPTPTPTPTPCPT)-3') ; × 1 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

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 7KUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 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
8CYF WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA Deposited 2022-05-23	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 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

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

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	Probable transcriptional regulator WhiB7 × 1 （Q6MX01） ;DNA (5'-D(CPAPGPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ; × 1 ;DNA (5'-D(GPAPCPCPAPCPAPAPCPCPGPAPTPTPTPTPCPT)-3') ; × 1 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

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 7KUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 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
8CYF WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA Deposited 2022-05-23	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 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

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	7kuf
Deposition date deposition_date	2020-11-24
Structure title title	Transcription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA
Keywords keywords	Redox-sensitive, Iron-sulfur cluster, transcription, activator; 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	21.30 Å
Radius of gyration Rg (electron density) rg_electron	20.40 Å
Forward intensity I(0) i0	23492100.00
Molecular weight molecular_weight	29117.0 kDa
Excluded volume excluded_volume	33009 Å³
Envelope volume envelope_volume	43031 Å³
Hydration-shell volume shell_volume	18289 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	26.05 Å
Envelope Rg envelope_rg	20.60 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	21.15 Å
Total atoms total_atoms	1987
Residues n_residues	194
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	69.7 Å
Rg (real space) rg_real	21.26 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.3490e+07
I(0) uncertainty (real space) i0_real_error	3.0630e+05
Rg (reciprocal space) rg_reciprocal	21.27 Å
I(0) (reciprocal space) i0_reciprocal	23490000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.405
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2074000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Probable transcriptional regulator WhiB7
Molecular weight formula_weight	10153.8 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	1987

MSVLTVPRQTPRQRLPVLPCHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGGEIFDQGSIVSHKRPRGRPRKDAVA

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
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(CPAPGPAPAPAPAPTPCPGPGPTPTPGPTPGPGPT)-3') ;
Molecular weight formula_weight	5595.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CAGAAAATCGGTTGTGGT

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(GPAPCPCPAPCPAPAPCPCPGPAPTPTPTPTPCPT)-3') ;
Molecular weight formula_weight	5435.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GACCACAACCGATTTTCT

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

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8. Citations (1)

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Unit-cell length a length_a	69.254 Å
Unit-cell length b length_b	69.254 Å
Unit-cell length c length_c	167.374 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.990 Å
R factor r_factor	0.2227
R_work r_work	0.2212
R_free r_free	0.2547

fit	/app/data/saxs_computation/ku/7kuf/7kuf.fit
pddf	/app/data/pr_computation/ku/7kuf/7kuf.pr.out
profile	/app/data/saxs_computation/ku/7kuf/7kuf.dat

Transcription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA

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

Probable transcriptional regulator WhiB7

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

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

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 (5)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)