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9rl0

CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus

Method: X-RAY DIFFRACTION D_max: 157.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rl0
deposition_date	2025-06-16
last_revision	2026-06-10
title	CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus
keywords	CDP-tyvelose 2-epimerase, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	47.70 Å
rg_electron	47.80 Å
i0	1365600000.00
molecular_weight	317070.0 kDa
excluded_volume	400280 Å³
envelope_volume	529690 Å³
shell_volume	89956 Å³
envelope_diameter	165.9 Å
shell_rg	53.70 Å
envelope_rg	47.45 Å
shape_rg	47.78 Å
total_rg	48.10 Å
total_atoms	22354
n_residues	2688
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	157.6 Å
rg_real	47.69 Å
rg_real_error	1.32 Å
i0_real	1.3660e+09
i0_real_error	2.4740e+07
rg_reciprocal	47.70 Å
i0_reciprocal	1366000000.0000
total_estimate	0.8767
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.3 Å
skewness	0.345
kurtosis	-0.291
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	173500000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.739

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	CDP-tyvelose 2-epimerase
formula_weight	39414.3 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	E,F,G,H,A,B,C,D
atom_count	22362

MKYLITGGCGFLGSNLASEVLRKREELIIFDNLYRIGSYENLEWLKQQGDFRFVHGDIRNREDIEKVIKEEKPDVIFHLAGQVAMTTSIENPRLDFEVNALGTFNLLDAVRKYSPESIIIYSSTNKVYGDLGWVRYEETETRYIAPDFPNGFPESIPLDFHSPYGCSKGAADQYMLDFCRIYGIKTVVFRHSSMYGGRQFATYDQGWIGWFCLKAIEIKKGLLKEPFTIHGNGKQVRDVLYADDMIELYFKTIENIEKAKGEAFNIGGGMENSLSLLELFSLLEKELDIKMRYKKLPWRESDQKIFVADIRKAQKLIGWQPKVSKYNGIQKMLEWIKKLV

Source

organism	Thermodesulfatator atlanticus
ncbi_taxonomy_id	501497
host_organism	Escherichia coli

Entity 2 non-polymer

description	CYTIDINE-5'-DIPHOSPHATE
formula_weight	403.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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length_a	132.415 Å
length_b	90.510 Å
length_c	133.624 Å
angle_alpha	90.00 °
angle_beta	101.19 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.600 Å
resolution_low	46.640 Å
r_factor	0.2438
r_work	0.2413
r_free	0.2893

fit	/app/data/saxs_computation/rl/9rl0/9rl0.fit
pddf	/app/data/pr_computation/rl/9rl0/9rl0.pr.out
profile	/app/data/saxs_computation/rl/9rl0/9rl0.dat

CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus

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