SAXSdb — 1dbd

▼

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

REGULATORY PROTEIN E2

Bovine papillomavirus type 1

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 311–410 Chain B； UniProt 311–410	Fragment：DNA-BINDING DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.75；308.3 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1	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 1DBD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JJH E2 DNA-binding Domain from Bovine Papillomavirus Type 1 Deposited 2001-07-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 326–410（85 aa） Fragment：DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；ammonium sulfate, imidazole, magnesium chloride, glycerol, DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.266
1JJH E2 DNA-binding Domain from Bovine Papillomavirus Type 1 Deposited 2001-07-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 326–410（85 aa） Fragment：DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；ammonium sulfate, imidazole, magnesium chloride, glycerol, DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.266
1JJH E2 DNA-binding Domain from Bovine Papillomavirus Type 1 Deposited 2001-07-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 326–410（85 aa） Fragment：DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；ammonium sulfate, imidazole, magnesium chloride, glycerol, DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.266
2BOP CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET Deposited 1994-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 326–410（85 aa）	Not recorded	YB YTTERBIUM (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.50, VAPOR DIFFUSION, HANGING DROP	Resolution 1.70 Å
2JEU Transcription activator structure reveals redox control of a replication initiation reaction Deposited 2007-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–209（209 aa） Fragment：N-TERMINAL TRANS-ACTIVATION DOMAIN (TAD), RESIDUES 1-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；PROTEIN WAS CRYSTALLISED FROM 0.1 M TRIS-HCL PH 8.5, 0.3 M NACL AND 18-22% TERTIARY BUTANOL, USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION.	Resolution 2.80 Å R-free 0.281
2JEX Transcription activator structure reveals redox control of a replication initiation reaction Deposited 2007-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–209（209 aa） Fragment：N-TERMINAL TRANS-ACTIVATION DOMAIN (TAD), RESIDUES 1-209	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；PROTEIN WAS CRYSTALLISED FROM 0.1 M TRIS-HCL PH 8.5, 0.3 M NACL, 2MM DTT AND 18-22% TERTIARY BUTANOL, USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION.	Resolution 2.35 Å R-free 0.241
6BUS Extended E2 DNA-binding domain of the Bovine Papillomavirus-1 Deposited 2017-12-11	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 310–410（101 aa） Fragment：UNP Residues 310-410 Chain 2 310–410（101 aa） Fragment：UNP Residues 310-410	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；sodium citrate, PEG 4000 and ammonium acetate	Resolution 1.90 Å R-free 0.261
6BUS Extended E2 DNA-binding domain of the Bovine Papillomavirus-1 Deposited 2017-12-11	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 3 310–410（101 aa） Fragment：UNP Residues 310-410 Chain 4 310–410（101 aa） Fragment：UNP Residues 310-410	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；sodium citrate, PEG 4000 and ammonium acetate	Resolution 1.90 Å R-free 0.261

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VE2_BPV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 311–410 Author chain B； PDBConstruct 1–100； UniProt 311–410

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	1dbd
Deposition date deposition_date	1999-05-21
Structure title title	E2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1
Keywords keywords	DNA-BINDING DOMAIN, GENE REGULATION; GENE REGULATION
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.09 Å
Radius of gyration Rg (electron density) rg_electron	17.82 Å
Forward intensity I(0) i0	10087300.00
Molecular weight molecular_weight	22480.0 kDa
Excluded volume excluded_volume	27807 Å³
Envelope volume envelope_volume	35639 Å³
Hydration-shell volume shell_volume	17052 Å³
Envelope diameter envelope_diameter	65.9 Å
Shell Rg shell_rg	23.63 Å
Envelope Rg envelope_rg	18.17 Å
Shape Rg shape_rg	17.78 Å
Total Rg total_rg	18.90 Å
Total atoms total_atoms	1584
Residues n_residues	200
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	65.5 Å
Rg (real space) rg_real	19.01 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.0090e+07
I(0) uncertainty (real space) i0_real_error	1.2090e+05
Rg (reciprocal space) rg_reciprocal	19.03 Å
I(0) (reciprocal space) i0_reciprocal	10090000.0000
Solution quality estimate total_estimate	0.8657
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.242
Kurtosis Kurtosis kurtosis	-0.277
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1563000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dbda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.8 — Viral DNA-binding domain
Family Family family	d.58.8.1 — Viral DNA-binding domain

Domain ID domain_id	d1dbdb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.8 — Viral DNA-binding domain
Family Family family	d.58.8.1 — Viral DNA-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1dbdA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	1dbdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

▶

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	REGULATORY PROTEIN E2
Molecular weight formula_weight	11249.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1584

来源生物 organism	Bovine papillomavirus type 1
NCBI Class编号 ncbi_taxonomy_id	10559
宿主生物 host_organism	Escherichia coli

E2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1

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

REGULATORY PROTEIN E2

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/db/1dbd/1dbd.fit
pddf	/app/data/pr_computation/db/1dbd/1dbd.pr.out
profile	/app/data/saxs_computation/db/1dbd/1dbd.dat