SAXSdb — 2e4p

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

Biphenyl dioxygenase ferredoxin subunit

Pseudomonas sp.

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–109	Not recorded	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；2.55M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.254
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–109	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；2.55M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.254

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 2E4P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2E4Q Crystal structure of BphA3 (reduced form) Deposited 2006-12-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–109（109 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.8M ammonium sulfate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.247
2E4Q Crystal structure of BphA3 (reduced form) Deposited 2006-12-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–109（109 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.8M ammonium sulfate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.247
2YVJ Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex Deposited 2007-04-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–109（109 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES, 30%(W/V) PEG4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.262

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BPHA3_PSES1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 1–109 Author chain B； PDBConstruct 1–109； UniProt 1–109

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	2e4p
Deposition date deposition_date	2006-12-15
Structure title title	Crystal structure of BphA3 (oxidized form)
Keywords keywords	Rieske type [2Fe-2S]cluster, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	22.82 Å
Radius of gyration Rg (electron density) rg_electron	22.63 Å
Forward intensity I(0) i0	11364700.00
Molecular weight molecular_weight	24167.0 kDa
Excluded volume excluded_volume	29717 Å³
Envelope volume envelope_volume	36122 Å³
Hydration-shell volume shell_volume	15000 Å³
Envelope diameter envelope_diameter	82.9 Å
Shell Rg shell_rg	26.81 Å
Envelope Rg envelope_rg	22.85 Å
Shape Rg shape_rg	22.70 Å
Total Rg total_rg	23.01 Å
Total atoms total_atoms	1678
Residues n_residues	216
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	82.2 Å
Rg (real space) rg_real	23.14 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.1360e+07
I(0) uncertainty (real space) i0_real_error	1.8000e+05
Rg (reciprocal space) rg_reciprocal	23.07 Å
I(0) (reciprocal space) i0_reciprocal	11360000.0000
Solution quality estimate total_estimate	0.7556
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.622
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2743000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.486; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.401; Smooth: 0.960

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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	Biphenyl dioxygenase ferredoxin subunit
Molecular weight formula_weight	11926.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1884

MTFTKACSVDEVPPGEALQVSHDAQKVAIFNVDGEFFATQDQCTHGEWSLSEGGYLDGDVVECSLHMGKFCVRTGKVKSPPPCEPLKVYPIRIEGRDVLVDFSRAALHA

来源 Source

来源生物 organism	Pseudomonas sp.
NCBI Class编号 ncbi_taxonomy_id	306
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	137

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2e4pa_
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.1 — Rieske iron-sulfur protein (ISP)

Domain ID domain_id	d2e4pb_
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.1 — Rieske iron-sulfur protein (ISP)

CATH v4.4 (2 domains)

Domain ID domain_id	2e4pA00
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

Domain ID domain_id	2e4pB00
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

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8. Citations (2)

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Unit-cell length a length_a	26.294 Å
Unit-cell length b length_b	144.113 Å
Unit-cell length c length_c	61.176 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	16.650 Å
R factor r_factor	0.2100
R_work r_work	0.2076
R_free r_free	0.2541

fit	/app/data/saxs_computation/e4/2e4p/2e4p.fit
pddf	/app/data/pr_computation/e4/2e4p/2e4p.pr.out
profile	/app/data/saxs_computation/e4/2e4p/2e4p.dat

Crystal structure of BphA3 (oxidized form)

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

Biphenyl dioxygenase ferredoxin 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