SAXSdb — 1i3s

▼

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

EARLY 35 KDA PROTEIN

Autographa californica nucleopolyhedrovirus

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 2–299	Mutation：YES	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；9-13% PEG 20,000, 100-400 mM NaCl, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.258
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–299	Mutation：YES	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；9-13% PEG 20,000, 100-400 mM NaCl, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.258
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2–299	Mutation：YES	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；9-13% PEG 20,000, 100-400 mM NaCl, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.258

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 1I3S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I3P THE 3.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE Deposited 2001-02-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–299（298 aa）	Mutation：V71P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；9-13% PEG 20,000, 100-400 mM NaCl, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.10 Å R-free 0.291
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–299（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å R-free 0.296
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–299（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å R-free 0.296
1P35 CRYSTAL STRUCTURE OF BACULOVIRUS P35 Deposited 1998-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–299（298 aa） Chain C 2–299（298 aa）	Not recorded	PO4 PHOSPHATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.20 Å R-free 0.262
1P35 CRYSTAL STRUCTURE OF BACULOVIRUS P35 Deposited 1998-09-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–299（298 aa）	Not recorded	PO4 PHOSPHATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.20 Å R-free 0.262
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–299（298 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K	Resolution 3.00 Å R-free 0.260
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–299（298 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K	Resolution 3.00 Å R-free 0.260

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP35_NPVAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–298； UniProt 2–299 Author chain B； PDBConstruct 1–298； UniProt 2–299 Author chain C； PDBConstruct 1–298； UniProt 2–299

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	1i3s
Deposition date deposition_date	2001-02-15
Structure title title	THE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE
Keywords keywords	hairpin loop, helix-turn-helix, reactive site loop, APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	41.60 Å
Radius of gyration Rg (electron density) rg_electron	42.05 Å
Forward intensity I(0) i0	133418000.00
Molecular weight molecular_weight	95443.0 kDa
Excluded volume excluded_volume	120030 Å³
Envelope volume envelope_volume	170960 Å³
Hydration-shell volume shell_volume	38283 Å³
Envelope diameter envelope_diameter	140.0 Å
Shell Rg shell_rg	41.33 Å
Envelope Rg envelope_rg	41.43 Å
Shape Rg shape_rg	42.06 Å
Total Rg total_rg	42.00 Å
Total atoms total_atoms	6727
Residues n_residues	846
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	142.6 Å
Rg (real space) rg_real	42.05 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	1.3340e+08
I(0) uncertainty (real space) i0_real_error	2.5670e+06
Rg (reciprocal space) rg_reciprocal	41.61 Å
I(0) (reciprocal space) i0_reciprocal	133400000.0000
Solution quality estimate total_estimate	0.7813
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.8 Å
Skewness Skewness skewness	0.528
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11300000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.646; Smooth: 0.614

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	EARLY 35 KDA PROTEIN
Molecular weight formula_weight	34743.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6781

CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTMLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKPDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIK

来源 Source

来源生物 organism	Autographa californica nucleopolyhedrovirus
NCBI Class编号 ncbi_taxonomy_id	46015
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1i3sa_
Class class	b — All beta proteins
Fold Fold fold	b.28 — Baculovirus p35 protein
Superfamily Superfamily superfamily	b.28.1 — Baculovirus p35 protein
Family Family family	b.28.1.1 — Baculovirus p35 protein

Domain ID domain_id	d1i3sb_
Class class	b — All beta proteins
Fold Fold fold	b.28 — Baculovirus p35 protein
Superfamily Superfamily superfamily	b.28.1 — Baculovirus p35 protein
Family Family family	b.28.1.1 — Baculovirus p35 protein

Domain ID domain_id	d1i3sc_
Class class	b — All beta proteins
Fold Fold fold	b.28 — Baculovirus p35 protein
Superfamily Superfamily superfamily	b.28.1 — Baculovirus p35 protein
Family Family family	b.28.1.1 — Baculovirus p35 protein

CATH v4.4 (3 domains)

Domain ID domain_id	1i3sA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	250 — Baculovirus p35
Homologous superfamily homologous superfamily	10 — Baculovirus p35

Domain ID domain_id	1i3sB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	250 — Baculovirus p35
Homologous superfamily homologous superfamily	10 — Baculovirus p35

Domain ID domain_id	1i3sC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	250 — Baculovirus p35
Homologous superfamily homologous superfamily	10 — Baculovirus p35

▶

8. Citations (2)

▶

Unit-cell length a length_a	77.608 Å
Unit-cell length b length_b	89.303 Å
Unit-cell length c length_c	136.099 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.490 Å
R factor r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2580

fit	/app/data/saxs_computation/i3/1i3s/1i3s.fit
pddf	/app/data/pr_computation/i3/1i3s/1i3s.pr.out
profile	/app/data/saxs_computation/i3/1i3s/1i3s.dat

THE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE

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

EARLY 35 KDA PROTEIN

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