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9x6i

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form)

Method: X-RAY DIFFRACTION D_max: 165.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x6i
deposition_date	2025-10-15
title	Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form)
keywords	short chain dehydrogenase /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	50.06 Å
rg_electron	49.96 Å
i0	1366500000.00
molecular_weight	298190.0 kDa
excluded_volume	369550 Å³
envelope_volume	521220 Å³
shell_volume	87127 Å³
envelope_diameter	169.1 Å
shell_rg	52.82 Å
envelope_rg	49.69 Å
shape_rg	49.97 Å
total_rg	49.99 Å
total_atoms	20902
n_residues	2852
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	165.4 Å
rg_real	50.08 Å
rg_real_error	1.92 Å
i0_real	1.3670e+09
i0_real_error	2.9460e+07
rg_reciprocal	50.03 Å
i0_reciprocal	1366000000.0000
total_estimate	0.8677
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.7 Å
skewness	0.353
kurtosis	-0.400
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	84520000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.665

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	22752

MRGSHHHHHHGSKNILITGGGSGVGRATARRFLIEGWQVGLIGRREDALQETAEDNPNALILPCDVTDEAAVDATFAKVASSWGRLDILFNNAGAVLPSTLIDEITVADWRRVTDVNITGMFLCARAAFRQMRNQQPMGGRIINNGSISADVPRPGSVPYTVSKHAVTGLTRTLSLDGRPFNIACGQVDIGNALTDMAVAMTKGVPQADGSTKIEPVIDVKTVADSVWHMATMPEGANIQWLTVMATNMPYIGRG

Source

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

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	18

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1826

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6. Citations (1)

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length_a	69.763 Å
length_b	73.454 Å
length_c	141.288 Å
angle_alpha	83.15 °
angle_beta	80.76 °
angle_gamma	83.81 °
z_pdb	12

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.900 Å
resolution_low	47.740 Å
r_factor	0.1701
r_work	0.1685
r_free	0.1993

fit	/app/data/saxs_computation/x6/9x6i/9x6i.fit
pddf	/app/data/pr_computation/x6/9x6i/9x6i.pr.out
profile	/app/data/saxs_computation/x6/9x6i/9x6i.dat