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1a62

CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO

Method: X-RAY DIFFRACTION Dmax: 53.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RHO

Escherichia coli BL21(DE3)

UniProt P03002

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 2–130 Fragment：RNA BINDING DOMAIN, RESIDUES 1 - 130 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0 Resolution 1.55 Å R-free 0.250

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 1A62 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A63 THE NMR STRUCTURE OF THE RNA BINDING DOMAIN OF E.COLI RHO FACTOR SUGGESTS POSSIBLE RNA-PROTEIN INTERACTIONS, 10 STRUCTURES Deposited 1998-03-05 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–130（130 aa） Fragment：RNA BINDING DOMAIN, RESIDUES 1 - 130
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K
Resolution not provided
1A8V STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERMINATOR Deposited 1998-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–118（118 aa） Fragment：RNA-BINDING DOMAIN
Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.00 Å R-free 0.261
1A8V STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERMINATOR Deposited 1998-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–118（118 aa） Fragment：RNA-BINDING DOMAIN
Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.00 Å R-free 0.261
2A8V RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX Deposited 1998-11-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–118（118 aa） Fragment：N-TERMINAL RNA BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.40 Å R-free 0.297
2A8V RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX Deposited 1998-11-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–118（118 aa） Fragment：N-TERMINAL RNA BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.40 Å R-free 0.297
2A8V RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX Deposited 1998-11-08 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–118（118 aa） Fragment：N-TERMINAL RNA BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.40 Å R-free 0.297

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

View Construct and Data Evidence
UniProt name RHO_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–130； UniProt 2–130

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 1a62

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a62
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a62
Deposition date deposition_date1998-03-05
Structure title titleCRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO
Keywords keywordsTRANSCRIPTION TERMINATION, TERMINATION, RNA BINDING DOMAIN, TRANSCRIPTION REGULATION, OB FOLD, F1-ATPASE; TRANSCRIPTION TERMINATION
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_guinier16.31 Å
Radius of gyration Rg (electron density) rg_electron15.02 Å
Forward intensity I(0) i04092440.00
Molecular weight molecular_weight14155.0 kDa
Excluded volume excluded_volume17631 ų
Envelope volume envelope_volume20418 ų
Hydration-shell volume shell_volume11988 ų
Envelope diameter envelope_diameter52.8 Å
Shell Rg shell_rg20.11 Å
Envelope Rg envelope_rg15.28 Å
Shape Rg shape_rg15.00 Å
Total Rg total_rg16.12 Å
Total atoms total_atoms987
Residues n_residues122
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 dmax53.9 Å
Rg (real space) rg_real16.28 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real4.0920e+06
I(0) uncertainty (real space) i0_real_error4.8710e+04
Rg (reciprocal space) rg_reciprocal16.28 Å
I(0) (reciprocal space) i0_reciprocal4092000.0000
Solution quality estimate total_estimate0.7299
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.0 Å
Skewness Skewness skewness0.307
Kurtosis Kurtosis kurtosis-0.278
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha770100.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 1.000; Smooth: 0.982
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1a62a1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1a62a2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like

CATH v4.4 (2 domains)

Domain ID domain_id1a62A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1a62A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (3)

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9. Files and Curves (10)