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6bog

Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription

Method: X-RAY DIFFRACTION Dmax: 150.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA polymerase-associated protein RapA

Escherichia coli O45:K1

UniProt B7MAI2

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 1–968 Fragment：Full-length Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；Ammonium sulfate, 1,4-Dioxane, Ethylene glycol, MES Resolution 3.21 Å R-free 0.279
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–968 Fragment：Full-length Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；Ammonium sulfate, 1,4-Dioxane, Ethylene glycol, MES Resolution 3.21 Å R-free 0.279

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 6BOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8T0L E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA Deposited 2023-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 2–967（966 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAPA_ECO45
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–968； UniProt 1–968 Author chain B； PDBConstruct 1–968； UniProt 1–968

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 6bog

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bog
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bog
Deposition date deposition_date2017-11-20
Structure title titleCrystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription
Keywords keywordshydrolase, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.89 Å
Radius of gyration Rg (electron density) rg_electron44.74 Å
Forward intensity I(0) i0793262000.00
Molecular weight molecular_weight222050.0 kDa
Excluded volume excluded_volume273250 ų
Envelope volume envelope_volume389050 ų
Hydration-shell volume shell_volume74045 ų
Envelope diameter envelope_diameter147.3 Å
Shell Rg shell_rg48.27 Å
Envelope Rg envelope_rg44.06 Å
Shape Rg shape_rg44.72 Å
Total Rg total_rg44.99 Å
Total atoms total_atoms15473
Residues n_residues1888
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 dmax150.4 Å
Rg (real space) rg_real44.92 Å
Rg uncertainty (real space) rg_real_error1.50 Å
I(0) (real space) i0_real7.9330e+08
I(0) uncertainty (real space) i0_real_error1.4520e+07
Rg (reciprocal space) rg_reciprocal44.89 Å
I(0) (reciprocal space) i0_reciprocal793200000.0000
Solution quality estimate total_estimate0.8140
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.6 Å
Skewness Skewness skewness0.359
Kurtosis Kurtosis kurtosis-0.395
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha123900000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id6bogA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6bogA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily930 —
Domain ID domain_id6bogA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10810 — Tandem AAA-ATPase domain
Domain ID domain_id6bogA05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6bogA06
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2230 —
Domain ID domain_id6bogA07
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily80 —
Domain ID domain_id6bogA08
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1500 —
Domain ID domain_id6bogB01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6bogB02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily930 —
Domain ID domain_id6bogB04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10810 — Tandem AAA-ATPase domain
Domain ID domain_id6bogB05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6bogB06
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2230 —
Domain ID domain_id6bogB07
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily80 —
Domain ID domain_id6bogB08
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1500 —
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8. Citations (2)

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9. Files and Curves (10)