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2ly7

B-flap domain of RNA polymerase (B. subtilis)

Method: SOLUTION NMR Dmax: 70.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit beta

Bacillus subtilis

UniProt P37870

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 784–923 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Pressure ambient NMR sample composition：500 uM [U-100% 13C; U-100% 15N] b-flap, 20 mM potassium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% 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 2LY7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different construct 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 C 1–1193（1193 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 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 C 1–1193（1193 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 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 C 1–1193（1193 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 C 1–1193（1193 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 C 1–1193（1193 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 C 1–1193（1193 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

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOB_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–141； UniProt 784–923

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2ly7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ly7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ly7
Deposition date deposition_date2012-09-12
Structure title titleB-flap domain of RNA polymerase (B. subtilis)
Keywords keywordsRNA Polymerase, Transcription, Non-uniform sampling; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.10 Å
Radius of gyration Rg (electron density) rg_electron18.99 Å
Forward intensity I(0) i01397370000.00
Molecular weight molecular_weight307920.0 kDa
Excluded volume excluded_volume382390 ų
Envelope volume envelope_volume46021 ų
Hydration-shell volume shell_volume18652 ų
Envelope diameter envelope_diameter77.9 Å
Shell Rg shell_rg27.57 Å
Envelope Rg envelope_rg23.35 Å
Shape Rg shape_rg19.01 Å
Total Rg total_rg19.09 Å
Total atoms total_atoms43400
Residues n_residues2780
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.6 Å
Rg (real space) rg_real19.30 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real1.3970e+09
I(0) uncertainty (real space) i0_real_error2.2300e+07
Rg (reciprocal space) rg_reciprocal19.27 Å
I(0) (reciprocal space) i0_reciprocal1397000000.0000
Solution quality estimate total_estimate0.7233
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.6 Å
Skewness Skewness skewness0.618
Kurtosis Kurtosis kurtosis0.147
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha816000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.600; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.604; 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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2ly7A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily150 — RNA polymerase II, Rpb2 subunit, wall domain
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8. Citations (1)

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9. Files and Curves (10)