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9x4u

Crystal structure of Fgm3 in complex with PLP

Method: X-RAY DIFFRACTION D_max: 144.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x4u
deposition_date	2025-10-11
last_revision	2026-05-20
title	Crystal structure of Fgm3 in complex with PLP
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	43.80 Å
rg_electron	43.53 Å
i0	431195000.00
molecular_weight	175270.0 kDa
excluded_volume	220710 Å³
envelope_volume	275560 Å³
shell_volume	52271 Å³
envelope_diameter	144.1 Å
shell_rg	49.08 Å
envelope_rg	42.55 Å
shape_rg	43.51 Å
total_rg	43.84 Å
total_atoms	12384
n_residues	1588
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	144.7 Å
rg_real	43.90 Å
rg_real_error	1.15 Å
i0_real	4.3120e+08
i0_real_error	7.7880e+06
rg_reciprocal	43.80 Å
i0_reciprocal	431100000.0000
total_estimate	0.8025
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.2 Å
skewness	0.259
kurtosis	-0.785
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	111000000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Aminotransferase-like protein FGM3
formula_weight	45063.6 kDa
ec_number	2.-.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14586

MSSSSFSIENVRSQFPALEKRQIFGDNAGGSQVLGTVAKSITEYLIETNVQLGASYKTSTQSTAIFDNAYKAAAKYINAGIDEIVIGASTTQVFRNLAAALKLQPGDELILTNVDHESNIDPWLHYAALNNATIKWWTPSDLNNPKLDPEQLRSLLTNKTRLVACTHCSNILGTINNIKAIADVVHEIPGALLAVDGVAYAPHRAIDVKELGADFYAFSWYKVYGPHISLLYGSKAAQAQLSSLGHFFNPDGSLMDKLELAAASYELTQAIIPLTAYFGENPKQTWDAIAEHEQKLQTRLIEYLVSKPQITVYGETSTDKAVRVPTVSFTVEGMSSQSVVEAVEAVSHAGIRWGHFFSKRLVGSILGLSDDGVVRVSLVHYNTVEEVDQIIVALEMVLLEHHHHHHHH

Source

organism	Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)
common_name	Wheat head blight fungus, Fusarium graminearum
ncbi_taxonomy_id	229533
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2174

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6. Citations (1)

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length_a	69.804 Å
length_b	97.693 Å
length_c	124.678 Å
angle_alpha	90.00 °
angle_beta	93.72 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.670 Å
resolution_low	21.900 Å
r_factor	0.1793
r_work	0.1781
r_free	0.2033

fit	/app/data/saxs_computation/x4/9x4u/9x4u.fit
pddf	/app/data/pr_computation/x4/9x4u/9x4u.pr.out
profile	/app/data/saxs_computation/x4/9x4u/9x4u.dat

Crystal structure of Fgm3 in complex with PLP

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