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9ypm

MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound

Method: X-RAY DIFFRACTION D_max: 93.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ypm
deposition_date	2025-10-14
title	MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions 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	30.88 Å
rg_electron	29.83 Å
i0	203549000.00
molecular_weight	111590.0 kDa
excluded_volume	138340 Å³
envelope_volume	166010 Å³
shell_volume	44495 Å³
envelope_diameter	98.9 Å
shell_rg	38.46 Å
envelope_rg	29.94 Å
shape_rg	29.83 Å
total_rg	30.54 Å
total_atoms	7767
n_residues	941
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	93.4 Å
rg_real	30.70 Å
rg_real_error	0.48 Å
i0_real	2.0350e+08
i0_real_error	2.9440e+06
rg_reciprocal	30.78 Å
i0_reciprocal	203600000.0000
total_estimate	0.9071
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.3 Å
skewness	0.130
kurtosis	-0.529
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	56500000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	8119

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	J,K,L,M

LAR

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	15

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	12

Entity 5 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	36

Entity 7 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	270

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6. Citations (1)

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length_a	157.094 Å
length_b	157.094 Å
length_c	157.423 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	—

resolution	2.450 Å
resolution_low	90.760 Å
r_factor	0.1642
r_work	0.1626
r_free	0.1951

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

MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions 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 (8)

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 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)