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9x4w

Crystal structure of Fgm3 in complex with PLP and L-Arg

Method: X-RAY DIFFRACTION D_max: 90.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x4w
deposition_date	2025-10-11
last_revision	2026-05-20
title	Crystal structure of Fgm3 in complex with PLP and 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	27.93 Å
rg_electron	27.00 Å
i0	117962000.00
molecular_weight	87554.0 kDa
excluded_volume	110220 Å³
envelope_volume	124200 Å³
shell_volume	37431 Å³
envelope_diameter	94.8 Å
shell_rg	35.50 Å
envelope_rg	27.25 Å
shape_rg	26.96 Å
total_rg	27.92 Å
total_atoms	6184
n_residues	791
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	90.1 Å
rg_real	27.86 Å
rg_real_error	0.49 Å
i0_real	1.1800e+08
i0_real_error	1.7190e+06
rg_reciprocal	27.88 Å
i0_reciprocal	118000000.0000
total_estimate	0.8939
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.317
kurtosis	-0.378
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	73210000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	7072

MSSSSFSIENVRSQFPALEKRQIFGDNAGGSQVLGTVAKSITEYLIETNVQLGASYKTSTQSTAIFDNAYKAAAKYINAGIDEIVIGASTTQVFRNLAAALKLQPGDELILTNVDHESNIDPWLHYAALNNATIKWWTPSDLNNPKLDPEQLRSLLTNKTRLVACTHCSNILGTINNIKAIADVVHEIPGALLAVDGVAYAPHRAIDVKELGADFYAFSWYKVYGPHISLLYGSKAAQAQLSSLGHFFNPDGSLMDKLELAAASYELTQAIIPLTAYFGENPKQTWDAIAEHEQKLQTRLIEYLVSKPQITVYGETSTDKAVRVPTVSFTVEGMSSQSVVEAVEAVSHAGIRWGHFFSKRLVGSILGLSDDGVVRVSLVHYNTVEEVDQIIVALEMVLLEHHHHHHHH

Source

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

Entity 2 non-polymer

description	(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine
formula_weight	403.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	888

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6. Citations (1)

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length_a	69.313 Å
length_b	96.849 Å
length_c	69.713 Å
angle_alpha	90.00 °
angle_beta	116.60 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.860 Å
resolution_low	61.980 Å
r_factor	0.1681
r_work	0.1669
r_free	0.2042

fit	/app/data/saxs_computation/x4/9x4w/9x4w.fit
pddf	/app/data/pr_computation/x4/9x4w/9x4w.pr.out
profile	/app/data/saxs_computation/x4/9x4w/9x4w.dat

Crystal structure of Fgm3 in complex with PLP and L-Arg

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