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1b4u

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

Method: X-RAY DIFFRACTION D_max: 90.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b4u
deposition_date	1998-12-29
title	PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)
keywords	EXTRADIOL TYPE DIOXYGENASE, PROTOCATECHUATE, NON-HEME IRON PROTEIN, DIOXYGENASE; DIOXYGENASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	29.18 Å
rg_electron	28.07 Å
i0	146028000.00
molecular_weight	95422.0 kDa
excluded_volume	119100 Å³
envelope_volume	139400 Å³
shell_volume	40107 Å³
envelope_diameter	94.7 Å
shell_rg	36.56 Å
envelope_rg	28.15 Å
shape_rg	28.08 Å
total_rg	28.82 Å
total_atoms	6708
n_residues	860
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	90.5 Å
rg_real	29.10 Å
rg_real_error	0.48 Å
i0_real	1.4600e+08
i0_real_error	1.7720e+06
rg_reciprocal	29.14 Å
i0_reciprocal	146000000.0000
total_estimate	0.9040
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.257
kurtosis	-0.467
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	46090000.0000
n_real_points	55
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTOCATECHUATE 4,5-DIOXYGENASE
formula_weight	15567.5 kDa
ec_number	1.13.11.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	6897

MTEKKERIDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY

Source

organism	Sphingomonas paucimobilis
ncbi_taxonomy_id	13689
host_organism	Escherichia coli

Entity 2 polymer

description	PROTOCATECHUATE 4,5-DIOXYGENASE
formula_weight	33323.0 kDa
ec_number	1.13.11.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSLAQA

Source

organism	Sphingomonas paucimobilis
ncbi_taxonomy_id	13689
host_organism	Escherichia coli

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	3,4-DIHYDROXYBENZOIC ACID
formula_weight	154.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	189

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6. Citations (1)

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length_a	65.400 Å
length_b	66.500 Å
length_c	119.800 Å
angle_alpha	90.00 °
angle_beta	92.50 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	60.000 Å
r_factor	—
r_work	0.1610
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)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)