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1sg5

Solution structure of Yaeo, a Rho-specific inhibitor of transcription termination

Method: SOLUTION NMR Dmax: 54.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

orf, hypothetical protein

Escherichia coli

UniProt P0AFW8

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 1–84 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；303 K；Pressure ambient NMR sample composition：2mM YaeO, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3,90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：2mM YaeO,U-15N, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：2mM YaeO,U-15N, 13C, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：2mM YaeO, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 100% D20 | 100% D20 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 1SG5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8PTM Structure of the transcription termination factor Rho in complex with Rof and ADP Deposited 2023-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain a 2–84（83 aa）
Chain b 2–84（83 aa）
Chain c 2–84（83 aa）
Chain d 2–84（83 aa）
Chain e 2–84（83 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
8PTN Structure of the transcription termination factor Rho in complex with Rof Deposited 2023-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain a 2–84（83 aa）
Chain b 2–84（83 aa）
Chain c 2–84（83 aa）
Chain d 2–84（83 aa）
Chain e 2–84（83 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.30 Å
8PTO Structure of Rho pentamer in complex with Rof and ADP Deposited 2023-07-14 Different construct Different mutation/modification 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 a 2–84（83 aa）
Chain b 2–84（83 aa）
Chain c 2–84（83 aa）
Chain d 2–84（83 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.70 Å
8PTP Structure of Rho pentamer in complex with Rof Deposited 2023-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 2–84（83 aa）
Chain b 2–84（83 aa）
Chain c 2–84（83 aa）
Chain d 2–84（83 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.00 Å
8W8D Structural mechanism of inhibition of the Rho transcription termination factor by Rof Deposited 2023-09-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain a 1–84（84 aa）
Chain b 1–84（84 aa）
Chain c 1–84（84 aa）
Chain d 1–84（84 aa）
Chain e 1–84（84 aa）
Chain f 1–84（84 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ROF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–86； UniProt 1–84

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 1sg5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1sg5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1sg5
Deposition date deposition_date2004-02-23
Structure title titleSolution structure of Yaeo, a Rho-specific inhibitor of transcription termination
Keywords keywordsa+b protein, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, TRANSCRIPTION, PROTEIN BINDING; STRUCTURAL GENOMICS, TRANSCRIPTION, PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.19 Å
Radius of gyration Rg (electron density) rg_electron12.95 Å
Forward intensity I(0) i0566829000.00
Molecular weight molecular_weight193800.0 kDa
Excluded volume excluded_volume239480 ų
Envelope volume envelope_volume25616 ų
Hydration-shell volume shell_volume13802 ų
Envelope diameter envelope_diameter58.5 Å
Shell Rg shell_rg21.80 Å
Envelope Rg envelope_rg17.35 Å
Shape Rg shape_rg12.84 Å
Total Rg total_rg13.51 Å
Total atoms total_atoms26840
Residues n_residues1720
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 dmax54.0 Å
Rg (real space) rg_real13.23 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real5.6680e+08
I(0) uncertainty (real space) i0_real_error8.0000e+06
Rg (reciprocal space) rg_reciprocal13.23 Å
I(0) (reciprocal space) i0_reciprocal566800000.0000
Solution quality estimate total_estimate0.7439
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.7 Å
Skewness Skewness skewness0.504
Kurtosis Kurtosis kurtosis0.334
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha209700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.337; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.656; Smooth: 0.999
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1sg5a1
Class classb — All beta proteins
Fold Fold foldb.137 — Rof/RNase P subunit-like
Superfamily Superfamily superfamilyb.137.1 — Rof/RNase P subunit-like
Family Family familyb.137.1.2 — Rof-like

CATH v4.4 (1 domains)

Domain ID domain_id1sg5A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily400 — Rof-like
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8. Citations (1)

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9. Files and Curves (10)