SAXSdb — 9ujd

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1. Structure Basics

entry_id	9ujd
deposition_date	2025-04-17
last_revision	2025-12-31
title	Crystal structure of a Transaminase PaTA from Pseudonocardia ammonioxydans in complex with PLP and LLP
keywords	catalysis, complex, aminotransferase, TRANSFERASE; 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	33.85 Å
rg_electron	33.33 Å
i0	296034000.00
molecular_weight	137620.0 kDa
excluded_volume	171540 Å³
envelope_volume	209220 Å³
shell_volume	51183 Å³
envelope_diameter	113.8 Å
shell_rg	41.03 Å
envelope_rg	33.22 Å
shape_rg	33.37 Å
total_rg	33.74 Å
total_atoms	9729
n_residues	1287
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	105.8 Å
rg_real	33.75 Å
rg_real_error	0.70 Å
i0_real	2.9600e+08
i0_real_error	4.4230e+06
rg_reciprocal	33.81 Å
i0_reciprocal	296000000.0000
total_estimate	0.9015
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.5 Å
skewness	0.240
kurtosis	-0.457
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	119700000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Branched-chain amino acid aminotransferase
formula_weight	38132.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9765

MTLADSGTDFSTSNLVAVEPGAIREDTPPGSVIQYSDYELDTSSPYAGGAAWIEGEYVPASEARISIFDTGFGHSDLTYTVAHVWHGNIFRLADHIERLLDGARKLRLASPYDETEIAEIAKRCVGLSQLREAYVNITLTRGYGKRKGEKDLSKLTSQIYVYAIPYLWAFPPYEQIFGTSAVVPRHVQRAGRNTIDPTIKNYQWGDLTAASFEAKDRGARTGILLDADGCVAEGPGFNVVVVKDGALASPSRNALPGITRKTVFEIAHARGISAELRDVTSRELYDADELMAVTTAGGVTPITSLDGAAVGDGEPGPITVAIRDRFWALMDEPSDLIDTIRYDVDRLE

Source

organism	Pseudonocardia ammonioxydans
ncbi_taxonomy_id	260086
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Branched-chain amino acid aminotransferase
formula_weight	37904.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D

MTLADSGTDFSTSNLVAVEPGAIREDTPPGSVIQYSDYELDTSSPYAGGAAWIEGEYVPASEARISIFDTGFGHSDLTYTVAHVWHGNIFRLADHIERLLDGARKLRLASPYDETEIAEIAKRCVGLSQLREAYVNITLTRGYGKRKGEKDLSKLTSQIYVYAIPYLWAFPPYEQIFGTSAVVPRHVQRAGRNTIDPTIKNYQWGDLTAASFEAKDRGARTGILLDADGCVAEGPGFNVVVVKDGALASPSRNALPGITRKTVFEIAHARGISAELRDVTSRELYDADELMAVTTAGGVTPITSLDGAAVGDGEPGPITVAIRDRFWALMDEPSDLIDTIRYDVDRLE

Source

organism	Pseudonocardia ammonioxydans
ncbi_taxonomy_id	260086
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	237.198 Å
length_b	237.198 Å
length_c	237.198 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	72

space_group	I 2 3
int_tables_number	197
crystal_system	—

resolution	2.800 Å
resolution_low	23.490 Å
r_factor	0.2072
r_work	0.2051
r_free	0.2482

fit	/app/data/saxs_computation/uj/9ujd/9ujd.fit
pddf	/app/data/pr_computation/uj/9ujd/9ujd.pr.out
profile	/app/data/saxs_computation/uj/9ujd/9ujd.dat

Crystal structure of a Transaminase PaTA from Pseudonocardia ammonioxydans in complex with PLP and LLP

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)