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9y43

3-hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.

Method: X-RAY DIFFRACTION D_max: 114.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y43
deposition_date	2025-09-02
title	3-hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.
keywords	Carbon Fixation, HP/HB cycle, ACD, LIGASE; LIGASE
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	36.06 Å
rg_electron	35.74 Å
i0	326711000.00
molecular_weight	151510.0 kDa
excluded_volume	192180 Å³
envelope_volume	241010 Å³
shell_volume	55061 Å³
envelope_diameter	123.5 Å
shell_rg	42.89 Å
envelope_rg	35.64 Å
shape_rg	35.73 Å
total_rg	36.27 Å
total_atoms	10636
n_residues	1394
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	114.6 Å
rg_real	35.95 Å
rg_real_error	0.66 Å
i0_real	3.2670e+08
i0_real_error	5.4010e+06
rg_reciprocal	36.02 Å
i0_reciprocal	326700000.0000
total_estimate	0.8990
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.9 Å
skewness	0.230
kurtosis	-0.415
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	71320000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.902

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	3-hydroxypropionate--CoA ligase [ADP-forming]
formula_weight	76234.9 kDa
ec_number	6.2.1.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10798

MAAVKKIFDEIIETDHKVITEESSKSILKNYGVKVPPYALVTSAEEAAKEAKKIGFPLVMKVVSPQILHKTDVGGVKVGLDNVADVKKTFTDMYGRLSKKKGVNVKGILLEKMVPKGVELIVGIQNDSQFGPIIMVGMGGIMTEVMKDVAFRMLPITTSDAKSMLNELKGSKLLKGFRGSEPIDTNLVAKMLVNIGKLGVENADYINSIDFNPVIVYPKSHYVVDAKIILNKEKKKNSISKAKPSITDMETFFTPKSVALVGASASPGKIGNSILDSLVNYDFKGKVYPINPKADKIFGQKCYPSVADIPGKVDLVVVSVDLSMTPPVLEDCAKKGVHSVVIVSGGGKELGGERAAYEAEVARLSKKHKIRIIGPNCIGMFNAANRLDCAFQGQERMVRSKLGPVAFFSQSGTMGISMLESADTFGLSKMISFGNRSDVDEADMIWYAANDPQTKVIGLYVEGFGDGRKFINVAKRVMKEKKKPIVIWKSGRTAAGAKQAASHTGSLGGSNAIIMGAFKQAGIISVDSYQELAGVLKALAWQPAAKGNKVAMTSNGAGPMIGGIDQLEKFGLAIGKLSPKLLKKMKSRFPPAVPIHNGNPADVGGGATADDYQFVIQQFMDEKNIDIAMPWFVFQDDPLEETIVDHLAGFQKKAKKPLLCGGNGGPYTEKMIKLIEKHNVPVYQDLRTWVAAASALHQWGKISKK

Source

organism	Nitrosopumilus maritimus SCM1
ncbi_taxonomy_id	436308
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	3-HYDROXY-PROPANOIC ACID
formula_weight	90.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	134

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6. Citations (1)

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length_a	81.876 Å
length_b	127.591 Å
length_c	137.764 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.800 Å
resolution_low	48.720 Å
r_factor	0.2133
r_work	0.2112
r_free	0.2542

fit	/app/data/saxs_computation/y4/9y43/9y43.fit
pddf	/app/data/pr_computation/y4/9y43/9y43.pr.out
profile	/app/data/saxs_computation/y4/9y43/9y43.dat