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9y83

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans

Method: X-RAY DIFFRACTION D_max: 122.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y83
deposition_date	2025-09-11
last_revision	2025-09-24
title	Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, 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	37.77 Å
rg_electron	37.32 Å
i0	330928000.00
molecular_weight	145590.0 kDa
excluded_volume	181210 Å³
envelope_volume	232900 Å³
shell_volume	52812 Å³
envelope_diameter	132.6 Å
shell_rg	42.63 Å
envelope_rg	37.02 Å
shape_rg	37.31 Å
total_rg	37.67 Å
total_atoms	10248
n_residues	1306
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	122.8 Å
rg_real	37.76 Å
rg_real_error	0.93 Å
i0_real	3.3090e+08
i0_real_error	5.5920e+06
rg_reciprocal	37.77 Å
i0_reciprocal	330900000.0000
total_estimate	0.6747
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	46.8 Å
skewness	0.311
kurtosis	-0.363
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	88600000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 1.000; Smooth: 0.783

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ornithine carbamoyltransferase
formula_weight	38211.3 kDa
ec_number	2.1.3.3
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10268

MAHHHHHHFNVHNRSYLTLIEYTPRQIRYLLDLSRDLKRAKYAGTETPRLNGKNIALIFEKTSTRTRCAFEVAAHDQGAHVTYIDPNGSQIGHKESMKDTARVLGRMYDAIEYRGFGQEIVEELAKYAGVPVYNGLTDEFHPTQMLADVLTMHEFSDRPIHDIAYCYIGDAHNNTGNSLMIVGAKLGMDVRLCAPRCLWPHDELIEQCRAIAATTGARLTLTEKPEEAVKGVDFIYTDVWVSMGEPFEKWGARIEELLPYRVNAALLAASGNPRVKFMHCLPAFHDSNTHVGKQIADQYGLPNGVEVTDDVFESDASIVFEQAENRLHTIKAILVATLT

Source

organism	Paraburkholderia xenovorans LB400
ncbi_taxonomy_id	266265
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	20

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6. Citations (1)

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length_a	157.570 Å
length_b	157.570 Å
length_c	138.457 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	2.550 Å
resolution_low	48.600 Å
r_factor	0.1920
r_work	0.1902
r_free	0.2265

fit	/app/data/saxs_computation/y8/9y83/9y83.fit
pddf	/app/data/pr_computation/y8/9y83/9y83.pr.out
profile	/app/data/saxs_computation/y8/9y83/9y83.dat

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans

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