7rwi

Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198

Method: X-RAY DIFFRACTION Dmax: 173.1 Å Quality: GOOD

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

DNA-directed RNA polymerase subunit alpha

Mycobacterium tuberculosis

UniProt A5U8D3

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain A; UniProt 1–347 Chain B; UniProt 1–347 Not recorded DNA-directed RNA polymerase subunit beta × 1 (P9WGY8) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A045J9E2) DNA-directed RNA polymerase subunit omega × 1 (A0A045H2R3) RNA polymerase sigma factor × 1 (A0A045IR27) T DNA × 1 NT DNA × 1 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000 Resolution 3.70 Å R-free 0.245

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.

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOA_MYCTA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–347; UniProt 1–347 Author chain B; PDBConstruct 1–347; UniProt 1–347

DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis

UniProt P9WGY8

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain C; UniProt 1–1178 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A5U8D3) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A045J9E2) DNA-directed RNA polymerase subunit omega × 1 (A0A045H2R3) RNA polymerase sigma factor × 1 (A0A045IR27) T DNA × 1 NT DNA × 1 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000 Resolution 3.70 Å R-free 0.245

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.

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

View Construct and Data Evidence
UniProt name RPOB_MYCTO
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1178; UniProt 1–1178

;DNA-directed RNA polymerase subunit beta' ;

Mycobacterium tuberculosis

UniProt A0A045J9E2

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain D; UniProt 1–1316 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A5U8D3) DNA-directed RNA polymerase subunit beta × 1 (P9WGY8) DNA-directed RNA polymerase subunit omega × 1 (A0A045H2R3) RNA polymerase sigma factor × 1 (A0A045IR27) T DNA × 1 NT DNA × 1 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000 Resolution 3.70 Å R-free 0.245

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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045J9E2_MYCTX
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1316; UniProt 1–1316

DNA-directed RNA polymerase subunit omega

Mycobacterium tuberculosis

UniProt A0A045H2R3

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain E; UniProt 1–110 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A5U8D3) DNA-directed RNA polymerase subunit beta × 1 (P9WGY8) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A045J9E2) RNA polymerase sigma factor × 1 (A0A045IR27) T DNA × 1 NT DNA × 1 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000 Resolution 3.70 Å R-free 0.245

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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045H2R3_MYCTX
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–110; UniProt 1–110

RNA polymerase sigma factor

Mycobacterium tuberculosis

UniProt A0A045IR27

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain F; UniProt 1–177 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A5U8D3) DNA-directed RNA polymerase subunit beta × 1 (P9WGY8) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A045J9E2) DNA-directed RNA polymerase subunit omega × 1 (A0A045H2R3) T DNA × 1 NT DNA × 1 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000 Resolution 3.70 Å R-free 0.245

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045IR27_MYCTX
Isoform
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–177; UniProt 1–177

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 7rwi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7rwi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7rwi
Deposition date deposition_date2021-08-19
Structure title titleMycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198
Keywords keywords;Mycobacterium tuberculosis, RNA polymerase, transcription inhibitor, TNP-2198, open promoter complex, TRANSCRIPTION-INHIBITOR complex ;; TRANSCRIPTION/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.97
Radius of gyration Rg (electron density) rg_electron46.54
Forward intensity I(0) i01939120000.00
Molecular weight molecular_weight354650.0 kDa
Excluded volume excluded_volume439580 ų
Envelope volume envelope_volume614850 ų
Hydration-shell volume shell_volume105140 ų
Envelope diameter envelope_diameter182.3
Shell Rg shell_rg54.43
Envelope Rg envelope_rg46.49
Shape Rg shape_rg46.55
Total Rg total_rg46.76
Total atoms total_atoms24903
Residues n_residues3141
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax173.1
Rg (real space) rg_real46.86
Rg uncertainty (real space) rg_real_error1.35
I(0) (real space) i0_real1.9390e+09
I(0) uncertainty (real space) i0_real_error3.4100e+07
Rg (reciprocal space) rg_reciprocal46.97
I(0) (reciprocal space) i0_reciprocal1939000000.0000
Solution quality estimate total_estimate0.8230
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary56.0
Skewness Skewness skewness0.388
Kurtosis Kurtosis kurtosis0.080
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha490300000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.575; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7rwiB01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id7rwiD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id7rwiD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily30 — RNA polymerase Rpb1 funnel domain

8. Citations (1)

9. Files and Curves (10)