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9y8h

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate

Method: X-RAY DIFFRACTION D_max: 63.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y8h
deposition_date	2025-09-11
last_revision	2025-09-24
title	Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate
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	20.79 Å
rg_electron	19.60 Å
i0	25340800.00
molecular_weight	37270.0 kDa
excluded_volume	46059 Å³
envelope_volume	53345 Å³
shell_volume	22257 Å³
envelope_diameter	64.9 Å
shell_rg	26.52 Å
envelope_rg	19.89 Å
shape_rg	19.59 Å
total_rg	20.48 Å
total_atoms	2614
n_residues	327
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	63.9 Å
rg_real	20.66 Å
rg_real_error	0.28 Å
i0_real	2.5340e+07
i0_real_error	2.9570e+05
rg_reciprocal	20.69 Å
i0_reciprocal	25340000.0000
total_estimate	0.9020
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.158
kurtosis	-0.502
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	5477000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Ornithine carbamoyltransferase
formula_weight	38211.3 kDa
ec_number	2.1.3.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2625

MAHHHHHHFNVHNRSYLTLIEYTPRQIRYLLDLSRDLKRAKYAGTETPRLNGKNIALIFEKTSTRTRCAFEVAAHDQGAHVTYIDPNGSQIGHKESMKDTARVLGRMYDAIEYRGFGQEIVEELAKYAGVPVYNGLTDEFHPTQMLADVLTMHEFSDRPIHDIAYCYIGDAHNNTGNSLMIVGAKLGMDVRLCAPRCLWPHDELIEQCRAIAATTGARLTLTEKPEEAVKGVDFIYTDVWVSMGEPFEKWGARIEELLPYRVNAALLAASGNPRVKFMHCLPAFHDSNTHVGKQIADQYGLPNGVEVTDDVFESDASIVFEQAENRLHTIKAILVATLT

Source

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

Entity 2 non-polymer

description	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
formula_weight	141.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	4

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	11

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6. Citations (1)

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length_a	131.498 Å
length_b	131.498 Å
length_c	131.498 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	I 2 3
int_tables_number	197
crystal_system	—

resolution	2.670 Å
resolution_low	46.490 Å
r_factor	0.1965
r_work	0.1935
r_free	0.2515

fit	/app/data/saxs_computation/y8/9y8h/9y8h.fit
pddf	/app/data/pr_computation/y8/9y8h/9y8h.pr.out
profile	/app/data/saxs_computation/y8/9y8h/9y8h.dat