SAXSdb — 6bus

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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 1； UniProt 310–410 Chain 2； UniProt 310–410	Fragment：UNP Residues 310-410	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain 3； UniProt 310–410 Chain 4； UniProt 310–410	Fragment：UNP Residues 310-410	No other associated polymer	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

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 6BUS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DBD E2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1 Deposited 1999-05-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 311–410（100 aa） Fragment：DNA-BINDING DOMAIN Chain B 311–410（100 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.75；308.3 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1	Resolution not provided
1JJH E2 DNA-binding Domain from Bovine Papillomavirus Type 1 Deposited 2001-07-05	Different construct Different mutation/modification 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 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 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 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 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 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

5 other PDB entries and 7 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 1； PDBConstruct 3–103； UniProt 310–410 Author chain 2； PDBConstruct 3–103； UniProt 310–410 Author chain 3； PDBConstruct 3–103； UniProt 310–410 Author chain 4； PDBConstruct 3–103； UniProt 310–410

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6bus
Deposition date deposition_date	2017-12-11
Structure title title	Extended E2 DNA-binding domain of the Bovine Papillomavirus-1
Keywords keywords	Open reading frame, E2, BPV-1, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	26.07 Å
Radius of gyration Rg (electron density) rg_electron	25.40 Å
Forward intensity I(0) i0	30524400.00
Molecular weight molecular_weight	41447.0 kDa
Excluded volume excluded_volume	51500 Å³
Envelope volume envelope_volume	67805 Å³
Hydration-shell volume shell_volume	22882 Å³
Envelope diameter envelope_diameter	86.2 Å
Shell Rg shell_rg	31.63 Å
Envelope Rg envelope_rg	25.10 Å
Shape Rg shape_rg	25.39 Å
Total Rg total_rg	26.18 Å
Total atoms total_atoms	2921
Residues n_residues	371
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	82.1 Å
Rg (real space) rg_real	26.13 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.0520e+07
I(0) uncertainty (real space) i0_real_error	4.5810e+05
Rg (reciprocal space) rg_reciprocal	26.11 Å
I(0) (reciprocal space) i0_reciprocal	30520000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3917000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.978

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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6bus1_
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	d6bus2_
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	d6bus3_
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	d6bus4_
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 (4 domains)

Domain ID domain_id	6bus100
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	6bus200
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	6bus300
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	6bus400
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

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8. Citations (1)

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Unit-cell length a length_a	55.203 Å
Unit-cell length b length_b	55.203 Å
Unit-cell length c length_c	203.091 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	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	67.790 Å
R factor r_factor	0.2161
R_work r_work	0.2138
R_free r_free	0.2605

Description description	Regulatory protein E2
Molecular weight formula_weight	11577.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4
Atom count atom_count	3118

Extended E2 DNA-binding domain of the Bovine Papillomavirus-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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

fit	/app/data/saxs_computation/bu/6bus/6bus.fit
pddf	/app/data/pr_computation/bu/6bus/6bus.pr.out
profile	/app/data/saxs_computation/bu/6bus/6bus.dat