SAXSdb — 1b69

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

PROTEIN (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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 3–71	Fragment：N-TERMINAL DNA BINDING DOMAIN Mutation：C57A	;DNA (5'-D(GPAPGPTPAPGPTPAPAPAPTPTPC)-3') ; × 1 ;DNA (5'-D(GPAPAPTPTPTPAPCPTPAPCPTPC)-3') ; × 1	SOLUTION NMR NMR measurement conditions：pH 6；305 K	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 1B69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BB8 N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES Deposited 1998-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	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	Parsed fields agree	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
2BB8 N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	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

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	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 3–71

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	1b69
Deposition date deposition_date	1999-01-21
Structure title title	THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX
Keywords keywords	INTEGRASE, DNA BINDING, TRANSPOSITION, COMPLEX, BETA-SHEET RECOGNITION, INTEGRASE-DNA COMPLEX; INTEGRASE/DNA
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.51 Å
Radius of gyration Rg (electron density) rg_electron	15.48 Å
Forward intensity I(0) i0	8196470.00
Molecular weight molecular_weight	16078.0 kDa
Excluded volume excluded_volume	17974 Å³
Envelope volume envelope_volume	23317 Å³
Hydration-shell volume shell_volume	13042 Å³
Envelope diameter envelope_diameter	54.7 Å
Shell Rg shell_rg	20.90 Å
Envelope Rg envelope_rg	15.81 Å
Shape Rg shape_rg	15.40 Å
Total Rg total_rg	16.47 Å
Total atoms total_atoms	1991
Residues n_residues	95
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	55.3 Å
Rg (real space) rg_real	16.44 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	8.1960e+06
I(0) uncertainty (real space) i0_real_error	9.3230e+04
Rg (reciprocal space) rg_reciprocal	16.44 Å
I(0) (reciprocal space) i0_reciprocal	8196000.0000
Solution quality estimate total_estimate	0.8839
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.9 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1317000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(GPAPGPTPAPGPTPAPAPAPTPTP*C)-3') ;
Molecular weight formula_weight	4014.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	1991

GAGTAGTAAATTC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPAPTPTPTPAPCPTPAPCPTP*C)-3') ;
Molecular weight formula_weight	3925.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAATTTACTACTC

Entity 3 Entity 3 polymer

Description description	PROTEIN (INTEGRASE)
Molecular weight formula_weight	8177.3 kDa
Mutation mutation	C57A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

EKRRDNRGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDAISLREKIAELQKDI

来源 Source

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)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b69a_
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	1b69A00
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

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8. Citations (1)

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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	—

fit	/app/data/saxs_computation/b6/1b69/1b69.fit
pddf	/app/data/pr_computation/b6/1b69/1b69.pr.out
profile	/app/data/saxs_computation/b6/1b69/1b69.dat

THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX

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

PROTEIN (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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 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)