SAXSdb — 6fi7

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

RNA polymerase sigma factor RpoS

Escherichia coli

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 245–330	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 350；Pressure 1 NMR sample composition：1 mM [U-99% 13C; U-99% 15N] E.coli Sigma factor S region 4, 93% H2O/7% D2O \| 93% H2O/7% 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 6FI7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IPL SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–330（330 aa）	Not recorded	DPO DIPHOSPHATE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.60 Å R-free 0.293
5IPM SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–330（330 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.20 Å R-free 0.330
5IPN SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–330（330 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.61 Å R-free 0.345
6KJ6 cryo-EM structure of Escherichia coli Crl transcription activation complex Deposited 2019-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain F 1–330（330 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 8 seconds before plunging	Resolution 3.80 Å
6UTV E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP, UTP, GTP, and ddATP for 150 seconds) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 DPO DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.45 Å R-free 0.348
6UTW E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 DPO DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.85 Å R-free 0.329
6UTX E. coli sigma-S transcription initiation complex with an empty bubble ("Old" crystal) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.05 Å R-free 0.349
6UTY E. coli sigma-S transcription initiation complex with a mismatching CTP ("Old" crystal soaked with CTP for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.15 Å R-free 0.370
6UTZ E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP and UTP for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 DPO DIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.80 Å R-free 0.343
6UU0 E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching GTP ("Fresh" crystal soaked with GTP for 1 hour) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.90 Å R-free 0.368
6UU1 E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Fresh" crystal soaked with CTP, GTP, and ddTTP for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.10 Å R-free 0.396
6UU2 E. coli sigma-S transcription initiation complex with 3-nt RNA ("Old" crystal soaked with GTP and ATP for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.40 Å R-free 0.363
6UU3 E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 D4M [(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.00 Å R-free 0.380
6UU4 E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.30 Å R-free 0.364
6UU5 E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 DPO DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 5.40 Å R-free 0.362
6UU6 E. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, and dinucleotide ApG for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	UTP URIDINE 5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.20 Å R-free 0.389
6UU7 E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG for 30 minutes) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.40 Å R-free 0.390
6UUA E. coli sigma-S transcription initiation complex with a mismatching CTP ("Fresh" crystal soaked with CTP for 2 hours) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain FFF 1–328（328 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.00 Å R-free 0.365
6UUB E. coli sigma-S transcription initiation complex with a mismatching UTP ("Fresh" crystal soaked with UTP for 2 hours) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 3.96 Å R-free 0.375
6UUC E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching ATP ("Fresh" crystal soaked with ATP for 2 hours) Deposited 2019-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain FFF 1–328（328 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES	Resolution 4.10 Å R-free 0.380

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 245–330

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	6fi7
Deposition date deposition_date	2018-01-17
Structure title title	E.coli Sigma factor S (RpoS) Region 4
Keywords keywords	Apo-RpoS region 4, Free RpoS region4, RNA binding protein; RNA BINDING 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	12.89 Å
Radius of gyration Rg (electron density) rg_electron	12.27 Å
Forward intensity I(0) i0	150146000.00
Molecular weight molecular_weight	100250.0 kDa
Excluded volume excluded_volume	124870 Å³
Envelope volume envelope_volume	16485 Å³
Hydration-shell volume shell_volume	10876 Å³
Envelope diameter envelope_diameter	44.0 Å
Shell Rg shell_rg	18.65 Å
Envelope Rg envelope_rg	13.36 Å
Shape Rg shape_rg	12.25 Å
Total Rg total_rg	12.53 Å
Total atoms total_atoms	14240
Residues n_residues	860
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	44.2 Å
Rg (real space) rg_real	12.85 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.5010e+08
I(0) uncertainty (real space) i0_real_error	1.9970e+06
Rg (reciprocal space) rg_reciprocal	12.85 Å
I(0) (reciprocal space) i0_reciprocal	150100000.0000
Solution quality estimate total_estimate	0.7637
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	14.5 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.306
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	176400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 0.962; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	RNA polymerase sigma factor RpoS
Molecular weight formula_weight	10041.4 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	14240

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/fi/6fi7/6fi7.fit
pddf	/app/data/pr_computation/fi/6fi7/6fi7.pr.out
profile	/app/data/saxs_computation/fi/6fi7/6fi7.dat

E.coli Sigma factor S (RpoS) Region 4

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

RNA polymerase sigma factor RpoS

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)