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9zpb

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

Method: X-RAY DIFFRACTION D_max: 119.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zpb
deposition_date	2025-12-16
last_revision	2025-12-24
title	Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP 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	37.33 Å
rg_electron	36.79 Å
i0	429829000.00
molecular_weight	164840.0 kDa
excluded_volume	204940 Å³
envelope_volume	256440 Å³
shell_volume	57046 Å³
envelope_diameter	127.0 Å
shell_rg	43.57 Å
envelope_rg	36.83 Å
shape_rg	36.79 Å
total_rg	37.16 Å
total_atoms	11564
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	119.3 Å
rg_real	37.23 Å
rg_real_error	0.75 Å
i0_real	4.2980e+08
i0_real_error	6.8380e+06
rg_reciprocal	37.30 Å
i0_reciprocal	429900000.0000
total_estimate	0.8965
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.6 Å
skewness	0.233
kurtosis	-0.494
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	70310000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.878

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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	12244

MAHHHHHHSPILPGAWLGMVGGGQLGRMFCFAAQAMGYRVAVLDPDENSPAGAVADRHLRAAYNDEASLTELARLCAAVSTEFENVPAASLDFLARTTFVSPAGRCVAVAQDRIAEKRFIASSGVTVAPHVVIESSDALAALDDAKLEAVLPGILKTARMGYDGKGQIRVRNAEEVREAHASLAGVPCVLEKRLPLKFEVSALIARAASGASVVYPLAQNTHRDGVLSHTIVPAPDASPTLVQQAQQAALQIADKLGYVGVLCVEFFILEDGSLVANEMAPRPHNSGHYTVDACATSQFEQQVRAMTGMPLGDTRQHSPAVMLNILGDVWFPDGPKRPAVTPPWQEVAAMPAARLHLYGKEEARCGRKMGHVNFTAATLEEARTAARDCARLLHIIT

Source

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

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

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

Entity 6 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	563

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6. Citations (1)

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length_a	67.005 Å
length_b	170.156 Å
length_c	170.322 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	2.190 Å
resolution_low	44.780 Å
r_factor	0.1752
r_work	0.1738
r_free	0.2040

fit	/app/data/saxs_computation/zp/9zpb/9zpb.fit
pddf	/app/data/pr_computation/zp/9zpb/9zpb.pr.out
profile	/app/data/saxs_computation/zp/9zpb/9zpb.dat