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1b4e

X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid

Method: X-RAY DIFFRACTION D_max: 79.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b4e
deposition_date	1998-12-19
title	X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid
keywords	DEHYDRATASE, LYASE; LYASE
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	21.44 Å
rg_electron	20.30 Å
i0	24234900.00
molecular_weight	36257.0 kDa
excluded_volume	44799 Å³
envelope_volume	52479 Å³
shell_volume	21705 Å³
envelope_diameter	81.4 Å
shell_rg	26.81 Å
envelope_rg	21.62 Å
shape_rg	20.28 Å
total_rg	21.19 Å
total_atoms	2522
n_residues	323
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	79.9 Å
rg_real	21.54 Å
rg_real_error	0.64 Å
i0_real	2.4230e+07
i0_real_error	3.1940e+05
rg_reciprocal	21.52 Å
i0_reciprocal	24230000.0000
total_estimate	0.7995
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.646
kurtosis	0.518
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	6866000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.508; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
formula_weight	35537.6 kDa
ec_number	4.2.1.24
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2893

TDLSQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLKEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	LAEVULINIC ACID
formula_weight	116.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	371

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6. Citations (1)

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length_a	126.700 Å
length_b	126.700 Å
length_c	141.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	—

resolution	2.000 Å
resolution_low	8.000 Å
r_factor	—
r_work	0.1880
r_free	0.2550

fit	/app/data/saxs_computation/b4/1b4e/1b4e.fit
pddf	/app/data/pr_computation/b4/1b4e/1b4e.pr.out
profile	/app/data/saxs_computation/b4/1b4e/1b4e.dat