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9ypl

MboA with Leu-Ala-Arg peptide substrate bound

Method: X-RAY DIFFRACTION D_max: 109.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ypl
deposition_date	2025-10-14
title	MboA with Leu-Ala-Arg peptide substrate bound
keywords	Heme-oxygenase like domain containing enzyme, HDO, Di-iron oxidase, alkynase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	32.87 Å
rg_electron	32.28 Å
i0	179015000.00
molecular_weight	107010.0 kDa
excluded_volume	133430 Å³
envelope_volume	164810 Å³
shell_volume	42738 Å³
envelope_diameter	118.8 Å
shell_rg	39.03 Å
envelope_rg	32.18 Å
shape_rg	32.27 Å
total_rg	32.83 Å
total_atoms	7497
n_residues	938
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	109.2 Å
rg_real	32.78 Å
rg_real_error	0.78 Å
i0_real	1.7900e+08
i0_real_error	2.6880e+06
rg_reciprocal	32.82 Å
i0_reciprocal	179000000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.2 Å
skewness	0.249
kurtosis	-0.406
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	50750000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Mangotoxin biosynthesis protein MboA
formula_weight	28433.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8203

MGHHHHHHHHHHSSGHLEVLFQGPHMISTAEMLKTLETTVDTCLEAEFKKDTVMGEFHKGDWFNESYYKRHILECVIRIHMNNELDARAVQVAAIDNISAAKQLSYYLYDEFGHDEMFGQDLITYGYSASDIKAEFAFPETWKLMGYLNFCVSKFGPLSSITWDWFLEYYGDKYSSFITQKASASMGQPAVSGAASHVAFDEAEDHSGMMNNMLSSVIKDEKDLAKAVVHIKAFVPMVGEYFQALRAATL

Source

organism	Pseudomonas syringae
ncbi_taxonomy_id	317
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	LEU-ALA-ARG peptide substrate
formula_weight	359.4 kDa
src_method	syn
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,J,K,L

LAR

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	14

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	595

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6. Citations (1)

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length_a	157.741 Å
length_b	157.741 Å
length_c	157.014 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	2.200 Å
resolution_low	43.750 Å
r_factor	0.1720
r_work	0.1713
r_free	0.1936

fit	/app/data/saxs_computation/yp/9ypl/9ypl.fit
pddf	/app/data/pr_computation/yp/9ypl/9ypl.pr.out
profile	/app/data/saxs_computation/yp/9ypl/9ypl.dat

MboA with Leu-Ala-Arg peptide substrate bound

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)