SAXSdb — 2a8v

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

RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR

OrganismNot specified

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–118	Fragment：N-TERMINAL RNA BINDING DOMAIN	5'-R(PCPCP*C)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 2.40 Å R-free 0.297
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–118	Fragment：N-TERMINAL RNA BINDING DOMAIN	5'-R(PCPCPCPCPCPC)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 2.40 Å R-free 0.297
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–118	Fragment：N-TERMINAL RNA BINDING DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 2.40 Å R-free 0.297

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 2A8V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A62 CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO Deposited 1998-03-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–130（129 aa） Fragment：RNA BINDING DOMAIN, RESIDUES 1 - 130	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.55 Å R-free 0.250
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 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 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 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

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RHO_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 1–118 Author chain B； PDBConstruct 1–118； UniProt 1–118 Author chain C； PDBConstruct 1–118； UniProt 1–118

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2a8v
Deposition date deposition_date	1998-11-08
Structure title title	RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX
Keywords keywords	RHO, OB FOLD, SINGLE-STRANDED NUCLEIC ACID BINDING DOMAIN, PROTEIN-RNA COMPLEX; PROTEIN/RNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	43.38 Å
Radius of gyration Rg (electron density) rg_electron	43.21 Å
Forward intensity I(0) i0	29662000.00
Molecular weight molecular_weight	42390.0 kDa
Excluded volume excluded_volume	52379 Å³
Envelope volume envelope_volume	95695 Å³
Hydration-shell volume shell_volume	18968 Å³
Envelope diameter envelope_diameter	122.6 Å
Shell Rg shell_rg	48.93 Å
Envelope Rg envelope_rg	39.41 Å
Shape Rg shape_rg	43.22 Å
Total Rg total_rg	43.49 Å
Total atoms total_atoms	2969
Residues n_residues	363
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	123.7 Å
Rg (real space) rg_real	43.27 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	2.9660e+07
I(0) uncertainty (real space) i0_real_error	4.5390e+05
Rg (reciprocal space) rg_reciprocal	43.38 Å
I(0) (reciprocal space) i0_reciprocal	29670000.0000
Solution quality estimate total_estimate	0.6450
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	75.6 Å
Skewness Skewness skewness	-0.276
Kurtosis Kurtosis kurtosis	-1.200
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	791700.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.052; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.606; Smooth: 0.621

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5'-R(PCPCP*C)-3'
Molecular weight formula_weight	870.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	3050

CCC

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	5'-R(PCPCPCPCPCPC)-3'
Molecular weight formula_weight	1786.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

CCCCCC

Entity 3 Entity 3 polymer

Description description	RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR
Molecular weight formula_weight	13218.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNE

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2a8va1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d2a8va2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2a8vb1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d2a8vb2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2a8vc1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d2a8vc2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	2a8vA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2a8vA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2a8vB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2a8vB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2a8vC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2a8vC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	132.783 Å
Unit-cell length b length_b	31.308 Å
Unit-cell length c length_c	105.751 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	14.000 Å
R factor r_factor	0.2455
R_work r_work	0.2455
R_free r_free	0.2970

fit	/app/data/saxs_computation/a8/2a8v/2a8v.fit
pddf	/app/data/pr_computation/a8/2a8v/2a8v.pr.out
profile	/app/data/saxs_computation/a8/2a8v/2a8v.dat

RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX

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

RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)