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1b4k

High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase

Method: X-RAY DIFFRACTION D_max: 84.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b4k
deposition_date	1998-12-22
title	High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase
keywords	LYASE, HEME BIOSYNTHESIS, MAGNESIUM, LEVULINIC ACID; 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	27.32 Å
rg_electron	26.28 Å
i0	85834300.00
molecular_weight	71522.0 kDa
excluded_volume	89095 Å³
envelope_volume	104770 Å³
shell_volume	32995 Å³
envelope_diameter	88.6 Å
shell_rg	34.14 Å
envelope_rg	26.55 Å
shape_rg	26.30 Å
total_rg	27.01 Å
total_atoms	5032
n_residues	646
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	84.7 Å
rg_real	27.32 Å
rg_real_error	0.53 Å
i0_real	8.5830e+07
i0_real_error	1.1160e+06
rg_reciprocal	27.32 Å
i0_reciprocal	85830000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.2 Å
skewness	0.376
kurtosis	-0.408
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	24730000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.880

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
formula_weight	37077.9 kDa
ec_number	4.2.1.24
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5604

MSFTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	208964
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	LAEVULINIC ACID
formula_weight	116.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	572

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6. Citations (1)

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length_a	128.240 Å
length_b	128.240 Å
length_c	86.220 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 4 21 2
int_tables_number	90
crystal_system	—

resolution	1.670 Å
resolution_low	51.300 Å
r_factor	—
r_work	0.1780
r_free	0.2080

fit	/app/data/saxs_computation/b4/1b4k/1b4k.fit
pddf	/app/data/pr_computation/b4/1b4k/1b4k.pr.out
profile	/app/data/saxs_computation/b4/1b4k/1b4k.dat