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9xax

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)

Method: X-RAY DIFFRACTION D_max: 172.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xax
deposition_date	2025-10-23
title	Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)
keywords	Short chain dihydrogenase/reductase superfamily, OXIDOREDUCTASE; OXIDOREDUCTASE
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	49.84 Å
rg_electron	49.85 Å
i0	1527450000.00
molecular_weight	308060.0 kDa
excluded_volume	378590 Å³
envelope_volume	518410 Å³
shell_volume	87700 Å³
envelope_diameter	177.9 Å
shell_rg	53.08 Å
envelope_rg	49.00 Å
shape_rg	49.86 Å
total_rg	49.92 Å
total_atoms	21564
n_residues	2833
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	172.8 Å
rg_real	49.94 Å
rg_real_error	1.96 Å
i0_real	1.5270e+09
i0_real_error	2.8200e+07
rg_reciprocal	49.84 Å
i0_reciprocal	1527000000.0000
total_estimate	0.8592
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.4 Å
skewness	0.411
kurtosis	-0.205
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	86430000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.808

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	SDR family NAD(P)-dependent oxidoreductase
formula_weight	27366.1 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	23163

MRGSHHHHHHGSKNILITGGGSGVGRATARRFLIEGWQVGLIGRREDALQETAEDNPNALILPCDVTDEAAVDATFAKVASSWGRLDILFNNAGAVLPSTLIDEITVADWRRVTDVNITGMFLCARAAFRQMRNQQPMGGRIINNGSISADVPRPGSVPYTVSKHAVTGLTRTLSLDGRPFNIACGQVDIGNALTDMAVAMTKGVPQADGSTKIEPVIDVKTVADSVWHMATMPEGANIQWLTVMATNMPYIGRG

Source

organism	Paracoccus litorisediminis
ncbi_taxonomy_id	2006130
host_organism	Escherichia coli DH5[alpha]

Entity 2 non-polymer

description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	743.4 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	TARTRONATE
formula_weight	118.0 kDa
src_method	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1599

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6. Citations (1)

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length_a	69.359 Å
length_b	72.552 Å
length_c	140.251 Å
angle_alpha	85.28 °
angle_beta	82.57 °
angle_gamma	84.52 °
z_pdb	12

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.080 Å
resolution_low	48.290 Å
r_factor	0.1703
r_work	0.1686
r_free	0.2007

fit	/app/data/saxs_computation/xa/9xax/9xax.fit
pddf	/app/data/pr_computation/xa/9xax/9xax.pr.out
profile	/app/data/saxs_computation/xa/9xax/9xax.dat

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)

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