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9zok

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ADP complex)

Method: X-RAY DIFFRACTION D_max: 120.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zok
deposition_date	2025-12-15
last_revision	2025-12-24
title	Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ADP complex)
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Phosphoribosylaminoimidazole carboxylase, LYASE ;; LYASE
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	37.29 Å
rg_electron	36.73 Å
i0	436540000.00
molecular_weight	165520.0 kDa
excluded_volume	205500 Å³
envelope_volume	256540 Å³
shell_volume	57101 Å³
envelope_diameter	127.2 Å
shell_rg	43.60 Å
envelope_rg	36.78 Å
shape_rg	36.74 Å
total_rg	37.11 Å
total_atoms	11605
n_residues	1549
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	120.3 Å
rg_real	37.18 Å
rg_real_error	1.12 Å
i0_real	4.3650e+08
i0_real_error	7.7530e+06
rg_reciprocal	37.25 Å
i0_reciprocal	436600000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.0 Å
skewness	0.227
kurtosis	-0.499
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	71650000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.920

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	N5-carboxyaminoimidazole ribonucleotide synthase
formula_weight	42509.5 kDa
ec_number	6.3.4.18
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12425

MAHHHHHHSPILPGAWLGMVGGGQLGRMFCFAAQAMGYRVAVLDPDENSPAGAVADRHLRAAYNDEASLTELARLCAAVSTEFENVPAASLDFLARTTFVSPAGRCVAVAQDRIAEKRFIASSGVTVAPHVVIESSDALAALDDAKLEAVLPGILKTARMGYDGKGQIRVRNAEEVREAHASLAGVPCVLEKRLPLKFEVSALIARAASGASVVYPLAQNTHRDGVLSHTIVPAPDASPTLVQQAQQAALQIADKLGYVGVLCVEFFILEDGSLVANEMAPRPHNSGHYTVDACATSQFEQQVRAMTGMPLGDTRQHSPAVMLNILGDVWFPDGPKRPAVTPPWQEVAAMPAARLHLYGKEEARCGRKMGHVNFTAATLEEARTAARDCARLLHIIT

Source

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

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	686

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6. Citations (1)

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length_a	66.914 Å
length_b	169.040 Å
length_c	170.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.090 Å
resolution_low	47.090 Å
r_factor	0.1697
r_work	0.1680
r_free	0.2042

fit	/app/data/saxs_computation/zo/9zok/9zok.fit
pddf	/app/data/pr_computation/zo/9zok/9zok.pr.out
profile	/app/data/saxs_computation/zo/9zok/9zok.dat