SAXSdb — 9vtk

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1. Structure Basics

entry_id	9vtk
deposition_date	2025-07-10
title	Structure of the family PL40 Ulvan Lyase Uly1040
keywords	Polysaccharide lyase, Family PL40 Ulvan lyase, 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	31.14 Å
rg_electron	30.67 Å
i0	132071000.00
molecular_weight	92050.0 kDa
excluded_volume	115220 Å³
envelope_volume	137800 Å³
shell_volume	37766 Å³
envelope_diameter	109.8 Å
shell_rg	37.42 Å
envelope_rg	30.73 Å
shape_rg	30.67 Å
total_rg	31.24 Å
total_atoms	12808
n_residues	803
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	103.4 Å
rg_real	31.25 Å
rg_real_error	0.73 Å
i0_real	1.3210e+08
i0_real_error	1.7790e+06
rg_reciprocal	31.20 Å
i0_reciprocal	132100000.0000
total_estimate	0.6678
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	32.5 Å
skewness	0.433
kurtosis	-0.388
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	31020000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.927; Smooth: 0.909

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Uly1040
formula_weight	97240.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14625

MKLTIKWAVCLLVVVTCTGEVSAQNVVRPSIWVTPSERQTILNKIERNEWAEKLFLSLQSRADAATSLTFEERREKLLDLPLVWSQSSENKQAPTLVTYTKGLGNQSDDKLRWGYPREPQEKMLKGIQDAVDCSVLYYLTQQDKYATCAADILAVFINALVQIPVNENGFMNSGWMYQDDHLLEARLVGAQLPIIYDFVYPFLKNGGQVLDVASNQLVDFDFSAAQKVFETYVYLALNRGLLESNWPVLESSSLLHNIHAHDDPQKVAELLPYYLDKNTQHQASLAMIAEMFKEPGDIWPESISYSKHVTSLSVYLMTLIDRKYPHYKVGSLYSNIPQSLTAMYNLQFPNDGYPYFGDTNRFMDVDFQAYEMALQLAKLNDNQEQIAQFSGVLRASIQNGEYERGKLPERDYYPSPYILPLTLLWSLDLQELEPLATDKSTVNKPQRPRSSHLPHAGLTIQRNLSQTDPVKNSLMTWVGGGSYIHGHASGMDMELYGQGYVLGIDGGKGTYRTDIHENYYRLFAAHNTVISNGASGSHGGWINMGINQVKTVAMEPAIDTQGASPNHSFATTEFYDEFNLVAPAQHQRTMALIRVNDKQGYYVDIFRAKSKASEEFHDYVYHNIGDAMDVVSNGRKVELAAEPERYQDSDKIKWEKHKAYQHPGWHFFKDVQSGKVSNQNFQVTFTANELEPHPIIMEAFIPEDSNIQFTQVSAPPSSAAAKPYNKKSLPSFLLRRQGEAWSNPFAVVYESYTQDDRQQGVVRKVERLMDDKVFKGLKVTLNVNGENLHQYVLVQNQDDDVYKNLALDIDFTGRFAVITVDSAGELLNAYIGKGHSLRYQDISLKTDKNQAIFKRF

Source

organism	Alteromonas macleodii
ncbi_taxonomy_id	28108
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	607

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6. Citations (1)

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length_a	48.997 Å
length_b	126.039 Å
length_c	69.737 Å
angle_alpha	90.00 °
angle_beta	97.96 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.740 Å
resolution_low	37.350 Å
r_factor	0.1854
r_work	0.1831
r_free	0.2269

fit	/app/data/saxs_computation/vt/9vtk/9vtk.fit
pddf	/app/data/pr_computation/vt/9vtk/9vtk.pr.out
profile	/app/data/saxs_computation/vt/9vtk/9vtk.dat

Structure of the family PL40 Ulvan Lyase Uly1040

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