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9yd7

Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate

Method: X-RAY DIFFRACTION D_max: 76.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yd7
deposition_date	2025-09-22
title	Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate
keywords	hydrolase, complex, Dihydroorotase, TIM BARREL; HYDROLASE
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	22.47 Å
rg_electron	21.47 Å
i0	37995400.00
molecular_weight	49033.0 kDa
excluded_volume	61887 Å³
envelope_volume	69298 Å³
shell_volume	26331 Å³
envelope_diameter	77.2 Å
shell_rg	28.97 Å
envelope_rg	21.82 Å
shape_rg	21.39 Å
total_rg	22.60 Å
total_atoms	3412
n_residues	422
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	76.2 Å
rg_real	22.40 Å
rg_real_error	0.42 Å
i0_real	3.8000e+07
i0_real_error	4.5130e+05
rg_reciprocal	22.42 Å
i0_reciprocal	38000000.0000
total_estimate	0.8721
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.295
kurtosis	-0.235
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	9525000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Dihydroorotase
formula_weight	48226.0 kDa
ec_number	3.5.2.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3674

MLLKNCRIIKDNKIIEGDILIDENGRIKKIAKDIKVDDEIIDIKNSLVIPGVIDAHVHFRWGEEKKEDFLSGSLAGINGGVCFAIDMPNNKPPITTKELFYKKLEDCKKDSKINVFLNFGVTENNYLGTVEDAKAYKIFMVKSVGDLFIEDYSKLKDILNQNKLFCIHAEHKDVINENLKKYQLNSWIDHCKIRDEKSEVEAVKEVIKNLKIIDRQSNKKPHVHFCHISTKEALYLIKKVRQELKNIKITVEVTPHHIYLNKDMAEELKGFGKFNPPLREKDDNIALIKGIVNKDVDIIASDHAPHLLEDKLKNVKNCPSGIPGIETIVPLTLNLVNKGLISLFDAIRVLSKNPAKIFNINNKIEEGNLANLTIIDLKKEGKINAELFKSKAKFSPFDGWEVKGFPIYTVINGTLYEAYGCKC

Source

organism	Methanocaldococcus jannaschii
ncbi_taxonomy_id	2190
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-CARBAMOYL-L-ASPARTATE
formula_weight	176.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	11

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	186

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6. Citations (1)

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length_a	111.380 Å
length_b	111.380 Å
length_c	101.220 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.870 Å
resolution_low	48.230 Å
r_factor	0.1694
r_work	0.1685
r_free	0.1863

fit	/app/data/saxs_computation/yd/9yd7/9yd7.fit
pddf	/app/data/pr_computation/yd/9yd7/9yd7.pr.out
profile	/app/data/saxs_computation/yd/9yd7/9yd7.dat

Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate

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