SAXSdb — 1byr

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

PROTEIN (ENDONUCLEASE)

Salmonella typhimurium

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–177	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；10 MG/ML PROTEIN + 2M NH4SO4, 100MM TRIS-HCL,PH 7.5	Resolution 2.00 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 1BYR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYS CRYSTAL STRUCTURE OF NUC COMPLEXED WITH TUNGSTATE Deposited 1998-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–177（155 aa）	Not recorded	WO4 TUNGSTATE(VI)ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10 MG/ML PROTEIN + 2M NH4SO4, 100MM TRIS-HCL, PH 7.5	Resolution 2.00 Å R-free 0.272

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q46707_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 23–177

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	1byr
Deposition date deposition_date	1998-10-19
Structure title title	CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D FAMILY MEMBER, NUC FROM SALMONELLA TYPHIMURIUM
Keywords keywords	ENDONUCLEASE, PHOSPHODIESTERASE; ENDONUCLEASE
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	15.51 Å
Radius of gyration Rg (electron density) rg_electron	14.24 Å
Forward intensity I(0) i0	5533610.00
Molecular weight molecular_weight	16790.0 kDa
Excluded volume excluded_volume	20943 Å³
Envelope volume envelope_volume	22528 Å³
Hydration-shell volume shell_volume	13274 Å³
Envelope diameter envelope_diameter	47.8 Å
Shell Rg shell_rg	20.22 Å
Envelope Rg envelope_rg	14.51 Å
Shape Rg shape_rg	14.23 Å
Total Rg total_rg	15.39 Å
Total atoms total_atoms	1245
Residues n_residues	152
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	48.3 Å
Rg (real space) rg_real	15.38 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	5.5340e+06
I(0) uncertainty (real space) i0_real_error	6.0940e+04
Rg (reciprocal space) rg_reciprocal	15.40 Å
I(0) (reciprocal space) i0_reciprocal	5534000.0000
Solution quality estimate total_estimate	0.8927
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.1 Å
Skewness Skewness skewness	0.033
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1268000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.986

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1byra_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.1 — Nuclease

CATH v4.4 (1 domains)

Domain ID domain_id	1byrA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

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8. Citations (1)

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Unit-cell length a length_a	59.060 Å
Unit-cell length b length_b	59.060 Å
Unit-cell length c length_c	111.300 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2500

Description description	PROTEIN (ENDONUCLEASE)
Molecular weight formula_weight	17175.4 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	1433

CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D FAMILY MEMBER, NUC FROM SALMONELLA TYPHIMURIUM

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

PROTEIN (ENDONUCLEASE)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

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)

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

fit	/app/data/saxs_computation/by/1byr/1byr.fit
pddf	/app/data/pr_computation/by/1byr/1byr.pr.out
profile	/app/data/saxs_computation/by/1byr/1byr.dat