SAXSdb — 1v0d

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

DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT

MUS MUSCULUS

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 1–329	Fragment：RESIDUES 1-329	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 PB LEAD (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 2.60 Å R-free 0.246

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 1V0D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9F NMR STRUCTURE OF THE CAD DOMAIN OF CASPASE-ACTIVATED DNASE Deposited 1999-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-87	Mutation：VPH ADDED AT N-TERMINUS	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure AMBIENT NMR sample composition U-15N NMR sample composition U-13C;U-15N NMR sample composition U-13C;U-15N NMR sample composition U-15N	Resolution not provided
1F2R NMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DOMAINS OF CAD AND ICAD Deposited 2000-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–87（87 aa） Fragment：N-TERMINAL DOMAIN (CAD DOMAIN), RESIDUES 1-87	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；308 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.6mM CAD U-15N,13C/0.6mM ICAD unlabeled; 20mM phophate buffer pH6.4 \| 90% H2O/10% D2O NMR sample composition 0.6mM CAD U-15N,13C/0.6mM ICAD unlabeled; 20mM phophate buffer pH6.4 \| 100% D2O NMR sample composition 0.6mM ICAD U-15N,13C/0.6mM CAD unlabeled; 20mM phophate buffer pH6.4 \| 90% H2O/10% D2O NMR sample composition 0.6mM ICAD U-15N,13C/0.6mM CAD unlabeled; 20mM phophate buffer pH6.4 \| 100% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DFFB_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 1–329

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	1v0d
Deposition date deposition_date	2004-03-26
Structure title title	Crystal Structure of Caspase-activated DNase (CAD)
Keywords keywords	HYDROLASE, NUCLEASE, CASPASE-ACTIVATED DNASE; HYDROLASE
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	22.58 Å
Radius of gyration Rg (electron density) rg_electron	22.00 Å
Forward intensity I(0) i0	14939800.00
Molecular weight molecular_weight	27766.0 kDa
Excluded volume excluded_volume	34183 Å³
Envelope volume envelope_volume	43831 Å³
Hydration-shell volume shell_volume	17865 Å³
Envelope diameter envelope_diameter	84.2 Å
Shell Rg shell_rg	27.39 Å
Envelope Rg envelope_rg	22.64 Å
Shape Rg shape_rg	22.01 Å
Total Rg total_rg	22.75 Å
Total atoms total_atoms	1939
Residues n_residues	245
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	82.4 Å
Rg (real space) rg_real	22.76 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.4940e+07
I(0) uncertainty (real space) i0_real_error	2.1750e+05
Rg (reciprocal space) rg_reciprocal	22.72 Å
I(0) (reciprocal space) i0_reciprocal	14940000.0000
Solution quality estimate total_estimate	0.8211
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	-0.009
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1796000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.762; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
Molecular weight formula_weight	37600.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1955

MCAVLRQPKCVKLRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCLYEDGTEVTDDCFPGLPNDAELLLLTAGETWHGYVSDITRFLSVFNEPHAGVIQAARQQLSDEQAPLRQKLLADLLHHVSQNITAETREQDPSWFEGLESRFRNKSGYLRYSCESRIRGYLREVSAYTSMVDEAAQEEYLRVLGSMCQKLKSVQYNGSYFDRGAEASSRLCTPEGWFSCQGPFDLESCLSKHSINPYGNRESRILFSTWNLDHIIEKKRTVVPTLAEAIQDGREVNWEYFYSLLFTAENLKLVHIACHKKTTHKLECDRSRIYRPQTGS

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	LEAD (II) ION
Molecular weight formula_weight	207.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1v0da_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.7 — Caspase-activated DNase, CAD (DffB, DFF40)

CATH v4.4 (1 domains)

Domain ID domain_id	1v0dA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	170 —

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8. Citations (1)

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Unit-cell length a length_a	110.189 Å
Unit-cell length b length_b	110.189 Å
Unit-cell length c length_c	73.982 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2460

fit	/app/data/saxs_computation/v0/1v0d/1v0d.fit
pddf	/app/data/pr_computation/v0/1v0d/1v0d.pr.out
profile	/app/data/saxs_computation/v0/1v0d/1v0d.dat

Crystal Structure of Caspase-activated DNase (CAD)

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

DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT

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