SAXSdb — 4nc8

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

DNA-directed RNA polymerase subunit delta

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–92	Fragment：UNP residues 2-92	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–92	Fragment：UNP residues 2-92	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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–92 Chain B； UniProt 2–92	Fragment：UNP residues 2-92	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

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 4NC8	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
2M4K Solution structure of the delta subunit of RNA polymerase from Bacillus subtilis Deposited 2013-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–173（172 aa）	Not recorded	No recorded non-water small molecule	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
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24	Different ligand/ion 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 ligand/ion 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 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 ligand/ion 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
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 ligand/ion 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 ligand/ion 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 10 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 1–91； UniProt 2–92 Author chain B； PDBConstruct 1–91； UniProt 2–92

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	4nc8
Deposition date deposition_date	2013-10-24
Structure title title	N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions
Keywords keywords	nucleus, TRANSCRIPTION; 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	20.34 Å
Radius of gyration Rg (electron density) rg_electron	19.46 Å
Forward intensity I(0) i0	6307360.00
Molecular weight molecular_weight	18666.0 kDa
Excluded volume excluded_volume	23531 Å³
Envelope volume envelope_volume	30829 Å³
Hydration-shell volume shell_volume	14527 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	23.99 Å
Envelope Rg envelope_rg	19.38 Å
Shape Rg shape_rg	19.45 Å
Total Rg total_rg	20.30 Å
Total atoms total_atoms	1316
Residues n_residues	158
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	68.2 Å
Rg (real space) rg_real	20.39 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	6.3070e+06
I(0) uncertainty (real space) i0_real_error	8.1770e+04
Rg (reciprocal space) rg_reciprocal	20.38 Å
I(0) (reciprocal space) i0_reciprocal	6307000.0000
Solution quality estimate total_estimate	0.8721
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1083000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.948

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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	DNA-directed RNA polymerase subunit delta
Molecular weight formula_weight	11769.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1344

GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQLEHHHHHH

来源 Source

来源生物 organism	Bacillus Subtilis
NCBI Class编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4nc8A00
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

Domain ID domain_id	4nc8B00
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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Unit-cell length a length_a	39.462 Å
Unit-cell length b length_b	109.636 Å
Unit-cell length c length_c	82.928 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.170 Å
Low-resolution limit resolution_low	41.500 Å
R factor r_factor	0.2268
R_work r_work	0.2239
R_free r_free	0.2826

fit	/app/data/saxs_computation/nc/4nc8/4nc8.fit
pddf	/app/data/pr_computation/nc/4nc8/4nc8.pr.out
profile	/app/data/saxs_computation/nc/4nc8/4nc8.dat

N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction