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9x51

Crystal structure of Fgm3 in complex with PLP and 4(S)-OH-L-Arg

Method: X-RAY DIFFRACTION D_max: 98.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x51
deposition_date	2025-10-14
last_revision	2026-05-20
title	Crystal structure of Fgm3 in complex with PLP and 4(S)-OH-L-Arg
keywords	PLP, Retro-aldol-like, Cbeta-Cgamma Bond Cleavage, 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	28.21 Å
rg_electron	27.24 Å
i0	120250000.00
molecular_weight	88218.0 kDa
excluded_volume	110960 Å³
envelope_volume	125950 Å³
shell_volume	37696 Å³
envelope_diameter	105.9 Å
shell_rg	35.65 Å
envelope_rg	27.55 Å
shape_rg	27.22 Å
total_rg	28.10 Å
total_atoms	6232
n_residues	796
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	98.0 Å
rg_real	28.16 Å
rg_real_error	0.60 Å
i0_real	1.2030e+08
i0_real_error	1.7730e+06
rg_reciprocal	28.18 Å
i0_reciprocal	120300000.0000
total_estimate	0.7884
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.345
kurtosis	-0.309
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	75320000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Aminotransferase-like protein FGM3
formula_weight	44835.4 kDa
ec_number	2.-.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7185

MSSSSFSIENVRSQFPALEKRQIFGDNAGGSQVLGTVAKSITEYLIETNVQLGASYKTSTQSTAIFDNAYKAAAKYINAGIDEIVIGASTTQVFRNLAAALKLQPGDELILTNVDHESNIDPWLHYAALNNATIKWWTPSDLNNPKLDPEQLRSLLTNKTRLVACTHCSNILGTINNIKAIADVVHEIPGALLAVDGVAYAPHRAIDVKELGADFYAFSWYKVYGPHISLLYGSKAAQAQLSSLGHFFNPDGSLMDKLELAAASYELTQAIIPLTAYFGENPKQTWDAIAEHEQKLQTRLIEYLVSKPQITVYGETSTDKAVRVPTVSFTVEGMSSQSVVEAVEAVSHAGIRWGHFFSKRLVGSILGLSDDGVVRVSLVHYNTVEEVDQIIVALEMVLLEHHHHHHHH

Source

organism	Fusarium graminearum PH-1
ncbi_taxonomy_id	229533
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	PYRIDOXAL-5'-PHOSPHATE
formula_weight	247.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(2S,4S)-4-hydroxy-L-arginine
formula_weight	190.2 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	939

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6. Citations (1)

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length_a	69.310 Å
length_b	97.400 Å
length_c	69.790 Å
angle_alpha	90.00 °
angle_beta	116.36 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.480 Å
resolution_low	59.090 Å
r_factor	0.1567
r_work	0.1558
r_free	0.1742

fit	/app/data/saxs_computation/x5/9x51/9x51.fit
pddf	/app/data/pr_computation/x5/9x51/9x51.pr.out
profile	/app/data/saxs_computation/x5/9x51/9x51.dat