SAXSdb — 1b4u

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

PROTOCATECHUATE 4,5-DIOXYGENASE

Sphingomonas paucimobilis

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–139 Chain C； UniProt 1–139	Fragment：CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN	PROTOCATECHUATE 4,5-DIOXYGENASE × 2 （P22636） FE FE (III) ION × 2 DHB 3,4-DIHYDROXYBENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.220

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 1B4U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOU THREE-DIMENSIONAL STRUCTURE OF LIGAB Deposited 1998-08-06	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–139（139 aa） Chain C 1–139（139 aa）	Not recorded	FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.206

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCYA_PSEPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 1–139 Author chain C； PDBConstruct 1–139； UniProt 1–139

PROTOCATECHUATE 4,5-DIOXYGENASE

Sphingomonas paucimobilis

UniProt P22636

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–302 Chain D； UniProt 1–302	Fragment：CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN	PROTOCATECHUATE 4,5-DIOXYGENASE × 2 （P22635） FE FE (III) ION × 2 DHB 3,4-DIHYDROXYBENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.220

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 1B4U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOU THREE-DIMENSIONAL STRUCTURE OF LIGAB Deposited 1998-08-06	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–302（302 aa） Chain D 1–302（302 aa）	Not recorded	FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.206

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCYB_PSEPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–302； UniProt 1–302 Author chain D； PDBConstruct 1–302； UniProt 1–302

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	1b4u
Deposition date deposition_date	1998-12-29
Structure title title	PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)
Keywords keywords	EXTRADIOL TYPE DIOXYGENASE, PROTOCATECHUATE, NON-HEME IRON PROTEIN, DIOXYGENASE; DIOXYGENASE
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	29.18 Å
Radius of gyration Rg (electron density) rg_electron	28.07 Å
Forward intensity I(0) i0	146028000.00
Molecular weight molecular_weight	95422.0 kDa
Excluded volume excluded_volume	119100 Å³
Envelope volume envelope_volume	139400 Å³
Hydration-shell volume shell_volume	40107 Å³
Envelope diameter envelope_diameter	94.7 Å
Shell Rg shell_rg	36.56 Å
Envelope Rg envelope_rg	28.15 Å
Shape Rg shape_rg	28.08 Å
Total Rg total_rg	28.82 Å
Total atoms total_atoms	6708
Residues n_residues	860
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	90.5 Å
Rg (real space) rg_real	29.10 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.4600e+08
I(0) uncertainty (real space) i0_real_error	1.7720e+06
Rg (reciprocal space) rg_reciprocal	29.14 Å
I(0) (reciprocal space) i0_reciprocal	146000000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.467
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46090000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.939

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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	PROTOCATECHUATE 4,5-DIOXYGENASE
Molecular weight formula_weight	15567.5 kDa
EC 编号 ec_number	1.13.11.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6897

MTEKKERIDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY

来源 Source

来源生物 organism	Sphingomonas paucimobilis
NCBI Class编号 ncbi_taxonomy_id	13689
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROTOCATECHUATE 4,5-DIOXYGENASE
Molecular weight formula_weight	33323.0 kDa
EC 编号 ec_number	1.13.11.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSLAQA

来源 Source

来源生物 organism	Sphingomonas paucimobilis
NCBI Class编号 ncbi_taxonomy_id	13689
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	3,4-DIHYDROXYBENZOIC ACID
Molecular weight formula_weight	154.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	189

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b4ua_
Class class	a — All alpha proteins
Fold Fold fold	a.88 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Superfamily Superfamily superfamily	a.88.1 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Family Family family	a.88.1.1 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB

Domain ID domain_id	d1b4ub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.6 — LigB-like
Family Family family	c.56.6.1 — LigB-like

Domain ID domain_id	d1b4uc_
Class class	a — All alpha proteins
Fold Fold fold	a.88 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Superfamily Superfamily superfamily	a.88.1 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Family Family family	a.88.1.1 — LigA subunit of an aromatic-ring-opening dioxygenase LigAB

Domain ID domain_id	d1b4ud_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.6 — LigB-like
Family Family family	c.56.6.1 — LigB-like

CATH v4.4 (4 domains)

Domain ID domain_id	1b4uA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	700 — Protocatechuate 4,5-dioxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Dioxygenase LigAB, LigA subunit

Domain ID domain_id	1b4uB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	830 — Protocatechuate 4,5-dioxygenase; Chain B
Homologous superfamily homologous superfamily	10 — LigB-like

Domain ID domain_id	1b4uC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	700 — Protocatechuate 4,5-dioxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Dioxygenase LigAB, LigA subunit

Domain ID domain_id	1b4uD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	830 — Protocatechuate 4,5-dioxygenase; Chain B
Homologous superfamily homologous superfamily	10 — LigB-like

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8. Citations (1)

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Unit-cell length a length_a	65.400 Å
Unit-cell length b length_b	66.500 Å
Unit-cell length c length_c	119.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	—
R_work r_work	0.1610
R_free r_free	0.2200

fit	/app/data/saxs_computation/b4/1b4u/1b4u.fit
pddf	/app/data/pr_computation/b4/1b4u/1b4u.pr.out
profile	/app/data/saxs_computation/b4/1b4u/1b4u.dat

PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)

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

PROTOCATECHUATE 4,5-DIOXYGENASE

State in the Current Structure

Other States of the Same Protein in the Database

PROTOCATECHUATE 4,5-DIOXYGENASE

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 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)