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9yb6

Human Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom.

Method: X-RAY DIFFRACTION D_max: 99.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yb6
deposition_date	2025-09-16
last_revision	2025-09-24
title	Human Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom.
keywords	Human Mitochondrial Aspartate Aminotransferase, GOT2, Glutamate Oxaloacetate Transaminase 2, Mitochondria, Transferase, AATM_human; TRANSFERASE
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	29.42 Å
rg_electron	28.44 Å
i0	131790000.00
molecular_weight	90600.0 kDa
excluded_volume	113220 Å³
envelope_volume	134390 Å³
shell_volume	38902 Å³
envelope_diameter	104.3 Å
shell_rg	36.16 Å
envelope_rg	28.63 Å
shape_rg	28.43 Å
total_rg	29.17 Å
total_atoms	6365
n_residues	803
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	99.0 Å
rg_real	29.40 Å
rg_real_error	0.68 Å
i0_real	1.3180e+08
i0_real_error	1.8600e+06
rg_reciprocal	29.41 Å
i0_reciprocal	131800000.0000
total_estimate	0.8815
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.360
kurtosis	-0.220
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	69120000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Aspartate aminotransferase, mitochondrial
formula_weight	47886.8 kDa
ec_number	2.6.1.1,2.6.1.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7496

MALLHSGRVLPGIAAAFHPGLAAAASMDMSSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALRIGASFLQRFFKFSRDVFLPKPTWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKNMGLYGERVGAFTMVCKDADEAKRVESQLKILIRPMYSNPPLNGARIAAAILNTPDLRKQWLQEVKVMADRIIGMRTQLVSNLKKEGSTHNWQHITDQIGMFCFTGLKPEQVERLIKEFSIYMTKDGRISVAGVTSSNVGYLAHAIHQVTK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	991

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6. Citations (1)

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length_a	57.180 Å
length_b	59.168 Å
length_c	67.167 Å
angle_alpha	101.39 °
angle_beta	101.72 °
angle_gamma	95.41 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.500 Å
resolution_low	48.515 Å
r_factor	—
r_work	0.1855
r_free	0.2094

fit	/app/data/saxs_computation/yb/9yb6/9yb6.fit
pddf	/app/data/pr_computation/yb/9yb6/9yb6.pr.out
profile	/app/data/saxs_computation/yb/9yb6/9yb6.dat