SAXSdb — 2m4k

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

DNA-directed RNA polymerase subunit delta

Bacillus subtilis subsp. 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–173	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.6；300 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition：10 % [U-100% 2H] D2O, 10 mM sodium chloride, 50 uM sodium azide, 20 mM sodium phosphate, 90 % H2O, 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 2M4K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KRC Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase Deposited 2009-12-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–92（91 aa） Fragment：residues 2-92	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；301 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 10 mM sodium chloride-1, 50 uM sodium azide-2, 20 mM phosphate buffer-3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium chloride-4, 50 uM sodium azide-5, 20 mM phosphate buffer-6, 14.29 mg/mL filamentous Pf1 bacteriophage-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium chloride-8, 50 uM sodium azide-9, 20 mM phosphate buffer-10, 5 % polyacrylamide gel-11, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–92（91 aa） Fragment：UNP residues 2-92 Chain B 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K	Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 2 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K	Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K	Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–92（91 aa） Fragment：UNP residues 2-92 Chain B 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 2 NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K	Resolution 2.00 Å R-free 0.259
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K	Resolution 2.17 Å R-free 0.283
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K	Resolution 2.17 Å R-free 0.283
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–92（91 aa） Fragment：UNP residues 2-92 Chain B 2–92（91 aa） Fragment：UNP residues 2-92	Not recorded	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K	Resolution 2.17 Å R-free 0.283
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28	Different construct 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 L 1–173（173 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain L 1–173（173 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain L 1–173（173 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 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 I 1–173（173 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

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOE_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–172； UniProt 2–173

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	2m4k
Deposition date deposition_date	2013-02-07
Structure title title	Solution structure of the delta subunit of RNA polymerase from Bacillus subtilis
Keywords keywords	delta subunit, RNA polymerase, transferase; TRANSFERASE
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	12.43 Å
Radius of gyration Rg (electron density) rg_electron	12.00 Å
Forward intensity I(0) i0	455978000.00
Molecular weight molecular_weight	188890.0 kDa
Excluded volume excluded_volume	239210 Å³
Envelope volume envelope_volume	18808 Å³
Hydration-shell volume shell_volume	11926 Å³
Envelope diameter envelope_diameter	43.1 Å
Shell Rg shell_rg	19.26 Å
Envelope Rg envelope_rg	13.59 Å
Shape Rg shape_rg	11.97 Å
Total Rg total_rg	12.24 Å
Total atoms total_atoms	26640
Residues n_residues	1620
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	36.4 Å
Rg (real space) rg_real	12.36 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	4.4480e+08
I(0) uncertainty (real space) i0_real_error	3.2640e+06
Rg (reciprocal space) rg_reciprocal	12.33 Å
I(0) (reciprocal space) i0_reciprocal	456000000.0000
Solution quality estimate total_estimate	0.7053
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.051
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	9.7200
Highest regularization parameter α highest_alpha	131100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 0.946; Sysdev: 0.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.605

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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2m4kA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1250 — RNA polymerase, subunit delta, N-terminal domain

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8. Citations (1)

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Description description	DNA-directed RNA polymerase subunit delta
Molecular weight formula_weight	20286.7 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	26640

来源生物 organism	Bacillus subtilis subsp. subtilis
NCBI Class编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/m4/2m4k/2m4k.fit
pddf	/app/data/pr_computation/m4/2m4k/2m4k.pr.out
profile	/app/data/saxs_computation/m4/2m4k/2m4k.dat

Solution structure of the delta subunit of RNA polymerase from Bacillus subtilis

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

DNA-directed RNA polymerase subunit delta

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

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)