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9ywn

Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase

Method: X-RAY DIFFRACTION D_max: 131.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ywn
deposition_date	2025-10-24
last_revision	2026-04-15
title	Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase
keywords	glycoside hydrolase, Xylanase, Endoxylanase, HYDROLASE; HYDROLASE
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	42.26 Å
rg_electron	41.65 Å
i0	1172700000.00
molecular_weight	285970.0 kDa
excluded_volume	358080 Å³
envelope_volume	447700 Å³
shell_volume	85388 Å³
envelope_diameter	137.6 Å
shell_rg	50.00 Å
envelope_rg	40.91 Å
shape_rg	41.61 Å
total_rg	42.14 Å
total_atoms	20217
n_residues	2543
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	131.1 Å
rg_real	42.00 Å
rg_real_error	1.02 Å
i0_real	1.1730e+09
i0_real_error	2.1570e+07
rg_reciprocal	42.26 Å
i0_reciprocal	1173000000.0000
total_estimate	0.8833
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.7 Å
skewness	0.096
kurtosis	-0.419
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	146300000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.892

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Glucuronoarabinoxylan endo-1,4-beta-xylanase
formula_weight	49706.9 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	22256

MHHHHHHSSGVDLGTENLYFQSNAMAYSVSVDINTSYQTLEGFGAAIAWSNESLTEHPNRAGLYKTLFFDSGLDILRLRNQYRNSSDFAYPDTEIVKLARCFNPNLKILLCSWTPPADIKENGVLNGGTLIKQNGAFVYDRFADYWYKSLNAYAAKGIVPDYISIQNEPDYQSSDWETCIFYPTETSNYPGYDKALDAVYSKLQTLPSMPKIIAAEATGIGTSMIGNNAAQQYFNKIDFSKIYGLAHHLYNGGDPNNPDSFNSVFKAIAAAYPGKPIFQTEYDQGTPFTTTQLIHNSLVEEGVSSYFFWDLIWDNSQRPMVIVEPPFNQNGWSNPQGYYKTDFYSSIQHYAKFTEPGYSRVKAESSGSNVSVTAFTSPGKDKLTLVLINKASSESTISLNLNGYTADTSAVYRTVFSGTAERFAHLGSLQGNTVTMPAQSVVTVALE

Source

organism	Anaerobacterium chartisolvens
ncbi_taxonomy_id	1297424
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	22

Entity 3 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	12

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1630

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6. Citations (1)

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length_a	89.307 Å
length_b	133.392 Å
length_c	137.700 Å
angle_alpha	90.00 °
angle_beta	101.54 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.916 Å
resolution_low	48.949 Å
r_factor	—
r_work	0.1686
r_free	0.2050

fit	/app/data/saxs_computation/yw/9ywn/9ywn.fit
pddf	/app/data/pr_computation/yw/9ywn/9ywn.pr.out
profile	/app/data/saxs_computation/yw/9ywn/9ywn.dat