5tjg

Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp

Method: X-RAY DIFFRACTION Dmax: 213.4 Å Quality: GOOD

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

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt Q9KWU8

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 1 PDB declaration: heptameric(7) Consistent with all polymer counts Chain A; UniProt 1–314 Chain B; UniProt 1–314 Not recorded DNA-directed RNA polymerase subunit beta × 1 (Q9KWU7) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9KWU6) DNA-directed RNA polymerase subunit omega × 1 (Q9EVV4) RNA polymerase sigma factor SigA × 1 (Q9EZJ8) ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') ; × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol Resolution 2.60 Å R-free 0.262

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.

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

View Construct and Data Evidence
UniProt name RPOA_THEAQ
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–314; UniProt 1–314 Author chain B; PDBConstruct 1–314; UniProt 1–314

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt Q9KWU7

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 1 PDB declaration: heptameric(7) Consistent with all polymer counts Chain C; UniProt 1–1119 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (Q9KWU8) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9KWU6) DNA-directed RNA polymerase subunit omega × 1 (Q9EVV4) RNA polymerase sigma factor SigA × 1 (Q9EZJ8) ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') ; × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol Resolution 2.60 Å R-free 0.262

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.

14 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOB_THEAQ
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1119; UniProt 1–1119

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt Q9KWU6

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 1 PDB declaration: heptameric(7) Consistent with all polymer counts Chain D; UniProt 1–1524 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (Q9KWU8) DNA-directed RNA polymerase subunit beta × 1 (Q9KWU7) DNA-directed RNA polymerase subunit omega × 1 (Q9EVV4) RNA polymerase sigma factor SigA × 1 (Q9EZJ8) ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') ; × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol Resolution 2.60 Å R-free 0.262

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.

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOC_THEAQ
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1524; UniProt 1–1524

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt Q9EVV4

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 1 PDB declaration: heptameric(7) Consistent with all polymer counts Chain E; UniProt 1–99 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (Q9KWU8) DNA-directed RNA polymerase subunit beta × 1 (Q9KWU7) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9KWU6) RNA polymerase sigma factor SigA × 1 (Q9EZJ8) ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') ; × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol Resolution 2.60 Å R-free 0.262

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.

11 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOZ_THEAQ
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–99; UniProt 1–99

RNA polymerase sigma factor SigA

Thermus aquaticus

UniProt Q9EZJ8

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 1 PDB declaration: heptameric(7) Consistent with all polymer counts Chain F; UniProt 92–438 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (Q9KWU8) DNA-directed RNA polymerase subunit beta × 1 (Q9KWU7) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9KWU6) DNA-directed RNA polymerase subunit omega × 1 (Q9EVV4) ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') ; × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol Resolution 2.60 Å R-free 0.262

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.

17 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SIGA_THEAQ
Isoform
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–347; UniProt 92–438

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 5tjg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tjg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tjg
Deposition date deposition_date2016-10-04
Structure title titleThermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp
Keywords keywordsRNA polymerase, Transferase-DNA complex; Transferase/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier54.14
Radius of gyration Rg (electron density) rg_electron54.64
Forward intensity I(0) i02168500000.00
Molecular weight molecular_weight391790.0 kDa
Excluded volume excluded_volume492310 ų
Envelope volume envelope_volume712320 ų
Hydration-shell volume shell_volume110420 ų
Envelope diameter envelope_diameter231.9
Shell Rg shell_rg56.94
Envelope Rg envelope_rg55.57
Shape Rg shape_rg54.66
Total Rg total_rg54.63
Total atoms total_atoms27590
Residues n_residues3474
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 dmax213.4
Rg (real space) rg_real54.57
Rg uncertainty (real space) rg_real_error2.50
I(0) (real space) i0_real2.1680e+09
I(0) uncertainty (real space) i0_real_error4.9260e+07
Rg (reciprocal space) rg_reciprocal53.82
I(0) (reciprocal space) i0_reciprocal2166000000.0000
Solution quality estimate total_estimate0.7735
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary66.2
Skewness Skewness skewness0.820
Kurtosis Kurtosis kurtosis0.954
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0005
Highest regularization parameter α highest_alpha255400000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.372; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.954

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id5tjgA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5tjgA02
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_id5tjgB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5tjgB02
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_id5tjgC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, subunit 2, domain 6
Domain ID domain_id5tjgC03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily10 — RNA polymerase Rpb2, domain 2
Domain ID domain_id5tjgC04
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, beta subunit, external 1 domain
Domain ID domain_id5tjgC05
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id5tjgC06
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
Domain ID domain_id5tjgD01
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_id5tjgD02
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
Domain ID domain_id5tjgE00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily10 — RNA polymerase subunit, RPB6/omega
Domain ID domain_id5tjgF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

8. Citations (1)

9. Files and Curves (10)