SAXSdb — 2bb8

▼

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

INTEGRASE

Enterococcus faecalis

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 3–73	Fragment：N-TERMINAL DNA BINDING DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；300 K NMR sample composition：H2O	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 2BB8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B69 THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX Deposited 1999-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 3–71（69 aa） Fragment：N-TERMINAL DNA BINDING DOMAIN	Mutation：C57A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K	Resolution not provided
1BB8 N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES Deposited 1998-04-29	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–73（71 aa） Fragment：N-TERMINAL DNA BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K NMR sample composition H2O	Resolution not provided
1TN9 THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX Deposited 1999-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 3–71（69 aa） Fragment：N-TERMINAL DNA BINDING DOMAIN	Mutation：C57A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K	Resolution not provided

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

View Construct and Data Evidence

UniProt name	TNR6_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–71； UniProt 3–73

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bb8
Deposition date deposition_date	1998-05-12
Structure title title	N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, MINIMIZED AVERAGE STRUCTURE
Keywords keywords	DNA RECOMBINATION, INTEGRASE, DNA BINDING, TRANSPOSITION, TRANSPOSASE; DNA RECOMBINATION
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.51 Å
Radius of gyration Rg (electron density) rg_electron	13.10 Å
Forward intensity I(0) i0	1673880.00
Molecular weight molecular_weight	8433.0 kDa
Excluded volume excluded_volume	10508 Å³
Envelope volume envelope_volume	12905 Å³
Hydration-shell volume shell_volume	8955 Å³
Envelope diameter envelope_diameter	46.2 Å
Shell Rg shell_rg	17.92 Å
Envelope Rg envelope_rg	13.54 Å
Shape Rg shape_rg	13.09 Å
Total Rg total_rg	14.37 Å
Total atoms total_atoms	1195
Residues n_residues	71
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

▼

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

Maximum dimension Dmax dmax	47.5 Å
Rg (real space) rg_real	14.49 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.6740e+06
I(0) uncertainty (real space) i0_real_error	2.1790e+04
Rg (reciprocal space) rg_reciprocal	14.50 Å
I(0) (reciprocal space) i0_reciprocal	1674000.0000
Solution quality estimate total_estimate	0.8971
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	337200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.981

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2bb8a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.10 — DNA-binding domain
Superfamily Superfamily superfamily	d.10.1 — DNA-binding domain
Family Family family	d.10.1.1 — DNA-binding domain from tn916 integrase

CATH v4.4 (1 domains)

Domain ID domain_id	2bb8A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	INTEGRASE
Molecular weight formula_weight	8462.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1195

来源生物 organism	Enterococcus faecalis
NCBI Class编号 ncbi_taxonomy_id	1351
宿主生物 host_organism	Escherichia coli BL21(DE3)

N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, MINIMIZED AVERAGE STRUCTURE

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

INTEGRASE

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/bb/2bb8/2bb8.fit
pddf	/app/data/pr_computation/bb/2bb8/2bb8.pr.out
profile	/app/data/saxs_computation/bb/2bb8/2bb8.dat