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9y4v

Crystal structure of a GH5_18 from Microbacterium oxydans DSM 20578

Method: X-RAY DIFFRACTION D_max: 101.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y4v
deposition_date	2025-09-03
title	Crystal structure of a GH5_18 from Microbacterium oxydans DSM 20578
keywords	glycoside hydrolase, N-glycan degradation, GH5, enzyme, CAZyme, 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	31.31 Å
rg_electron	30.75 Å
i0	129866000.00
molecular_weight	89705.0 kDa
excluded_volume	111540 Å³
envelope_volume	130650 Å³
shell_volume	36355 Å³
envelope_diameter	107.0 Å
shell_rg	36.92 Å
envelope_rg	31.07 Å
shape_rg	30.71 Å
total_rg	31.38 Å
total_atoms	6348
n_residues	822
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	101.6 Å
rg_real	31.49 Å
rg_real_error	0.73 Å
i0_real	1.2990e+08
i0_real_error	1.8650e+06
rg_reciprocal	31.41 Å
i0_reciprocal	129900000.0000
total_estimate	0.8526
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.9 Å
skewness	0.487
kurtosis	-0.402
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	48490000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.717

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glycosyl hydrolase
formula_weight	51336.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7186

MGSSHHHHHHSSGLVPRGSHMMTQRGALDAPLRFGANYTPSKNWMHSWLDFTPDDVRRDFATLAELGLDHVRVFPLWTVLQPNRTLIREKAIDDVRAVVDIAGEFGMDASIDVVQGHLSSFDFVPSWLYTWHDKNMFTDPRALEGQIALVDRLGRALSEAPNFLGLTLGNETNQFSAHTHPSPWPVTQDEAGGWISALLSAAEAAAPGLPHVHSEYDAVWYMDGHGFTPAHASRLGAMTTIHSWIFNGTAQRYGGRSVASDRHAEYLIELSRAFATDPDRVVWLQEVGAPSNCLTDDEMPGFLEATVRWAVRTENLWGITWWCSHDVSRDLGDFPELEYTLGLIGQDGAAKPIGRRLAELIPELRQRVAPPARDTAIVVDVDEREVPVSRAALSPGGAVFQAWVDACAAGLDPTLVTSHDALDPVALDARGIRRLIRPDLSADVVDPYGSVNTVVPGLEHHHHHH

Source

organism	Microbacterium oxydans
ncbi_taxonomy_id	82380
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	827

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6. Citations (1)

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length_a	81.237 Å
length_b	95.142 Å
length_c	102.056 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.920 Å
resolution_low	29.570 Å
r_factor	0.1726
r_work	0.1703
r_free	0.2158

fit	/app/data/saxs_computation/y4/9y4v/9y4v.fit
pddf	/app/data/pr_computation/y4/9y4v/9y4v.pr.out
profile	/app/data/saxs_computation/y4/9y4v/9y4v.dat

Crystal structure of a GH5_18 from Microbacterium oxydans DSM 20578

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