SAXSdb — 3gfk

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

Regulatory protein spx

Bacillus subtilis

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–131	Not recorded	DNA-directed RNA polymerase subunit alpha × 1 （P20429）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5；295 K；vapor diffusion against 6% (w/v) PEG 6000, 100 mM sodium acetate, pH 5.0, 10 micromolar CuCl2, protein concentration 11.5 mg/mL, temperature 295K	Resolution 2.30 Å R-free 0.282

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 3GFK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z3E Crystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit Deposited 2005-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa） Fragment：transcription regulator	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；273 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 273K	Resolution 1.50 Å R-free 0.220
3IHQ Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras Deposited 2009-07-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Mutation：C10S	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；273 K；25-30% PEG 4000, 0.1 M sodium citrate, 0.1 M magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.278
6GHB Crystal structure of Spx in complex with YjbH (oxidized) Deposited 2018-05-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266
6GHB Crystal structure of Spx in complex with YjbH (oxidized) Deposited 2018-05-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–131（131 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266
6GHO Crystal structure of Spx in complex with YjbH Deposited 2018-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 3350, MgCl2 and Bis-Tris pH 6.0	Resolution 1.79 Å R-free 0.221

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPX_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 1–131

DNA-directed RNA polymerase subunit alpha

Bacillus subtilis

UniProt P20429

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 240–314	Fragment：Alpha C-terminal domain (alpha-CTD)	Regulatory protein spx × 1 （O31602）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5；295 K；vapor diffusion against 6% (w/v) PEG 6000, 100 mM sodium acetate, pH 5.0, 10 micromolar CuCl2, protein concentration 11.5 mg/mL, temperature 295K	Resolution 2.30 Å R-free 0.282

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 3GFK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z3E Crystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit Deposited 2005-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 245–314（70 aa） Fragment：c-terminal domain of RNA polymerase alpha subunit	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；273 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 273K	Resolution 1.50 Å R-free 0.220
3IHQ Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras Deposited 2009-07-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 245–314（70 aa） Fragment：UNP residues 245-314	Not recorded	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；273 K；25-30% PEG 4000, 0.1 M sodium citrate, 0.1 M magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.278
6WVJ Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex Deposited 2020-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.	Resolution 3.36 Å
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06	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 × 7 PDB declaration: heptameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.	Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18	Different construct Different mutation/modification 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 A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa） Chain I 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02	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 × 8 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOA_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–79； UniProt 240–314

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	3gfk
Deposition date deposition_date	2009-02-27
Structure title title	Crystal structure of Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex
Keywords keywords	;protein-protein complex, Cytoplasm, Redox-active center, Stress response, Transcription, Transcription regulation, DNA-directed RNA polymerase, Nucleotidyltransferase, Transferase, Transcription-Transferase COMPLEX ;; Transcription/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	19.74 Å
Radius of gyration Rg (electron density) rg_electron	18.66 Å
Forward intensity I(0) i0	9644120.00
Molecular weight molecular_weight	22665.0 kDa
Excluded volume excluded_volume	28367 Å³
Envelope volume envelope_volume	35510 Å³
Hydration-shell volume shell_volume	16457 Å³
Envelope diameter envelope_diameter	63.6 Å
Shell Rg shell_rg	24.32 Å
Envelope Rg envelope_rg	19.00 Å
Shape Rg shape_rg	18.65 Å
Total Rg total_rg	19.61 Å
Total atoms total_atoms	1586
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	64.0 Å
Rg (real space) rg_real	19.69 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	9.6440e+06
I(0) uncertainty (real space) i0_real_error	1.0920e+05
Rg (reciprocal space) rg_reciprocal	19.70 Å
I(0) (reciprocal space) i0_reciprocal	9644000.0000
Solution quality estimate total_estimate	0.8934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.478
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	2747000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Regulatory protein spx
Molecular weight formula_weight	15551.9 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	1843

MVTLYTSPSCTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLPRKVRSFQLREAQRLAN

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	9118.5 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

GPHMKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	257

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3gfka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.12 — ArsC-like

Domain ID domain_id	d3gfkb1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3gfkb2
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	3gfkA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	3gfkB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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8. Citations (1)

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Unit-cell length a length_a	41.900 Å
Unit-cell length b length_b	44.300 Å
Unit-cell length c length_c	117.200 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	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2820

fit	/app/data/saxs_computation/gf/3gfk/3gfk.fit
pddf	/app/data/pr_computation/gf/3gfk/3gfk.pr.out
profile	/app/data/saxs_computation/gf/3gfk/3gfk.dat

Crystal structure of Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex

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

Regulatory protein spx

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase subunit alpha

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)