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9u77

Crystal structure of Glycogen branching enzyme (VvGBE) from Vibrio vulnificus MO6-24/O

Method: X-RAY DIFFRACTION D_max: 141.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u77
deposition_date	2025-03-24
last_revision	2026-02-04
title	Crystal structure of Glycogen branching enzyme (VvGBE) from Vibrio vulnificus MO6-24/O
keywords	glycogen branching enzyme, GH13_9, transferase; TRANSFERASE
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	40.06 Å
rg_electron	39.95 Å
i0	400500000.00
molecular_weight	164240.0 kDa
excluded_volume	205050 Å³
envelope_volume	256920 Å³
shell_volume	54362 Å³
envelope_diameter	151.1 Å
shell_rg	44.56 Å
envelope_rg	39.88 Å
shape_rg	39.89 Å
total_rg	40.40 Å
total_atoms	11642
n_residues	1434
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	141.2 Å
rg_real	40.14 Å
rg_real_error	1.66 Å
i0_real	4.0050e+08
i0_real_error	7.0570e+06
rg_reciprocal	40.06 Å
i0_reciprocal	400500000.0000
total_estimate	0.8605
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.1 Å
skewness	0.401
kurtosis	-0.227
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	89180000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.883

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	1,4-alpha-glucan branching enzyme GlgB
formula_weight	85139.7 kDa
ec_number	2.4.1.18
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11896

MRIVFTTLAVWRGKKGLKKLVKSKVNQMFEKLSQAACSEPFAFLGPFIDPTQGALRVWMPGATGVALVLEGQPRIALEREKESAFILKADLNLHLTHYQLAIDWNGVEQLIDDPYQYHGIYAEYDDLHTPKTMYQHMGSQFMTLERDGKSISGIRFLVYAPHATAVSLVGCFNDWDGRRHPMQRLDYGIWGLFIPGLTEGVSYKFEMKGPKGEGLPHKADPWGFYAEQYPSFASVTYDHARYQWQDAQWQTRPVTEKRKEALSFYELHAGSWKRNEQGEFLNYRELAAELVPYLVDMGYTHVELMPVSEHPFYGSWGYQPVGLFAPTSRYGSPDDFKFFVDACHQAGIGVVLDWVPAHFPSDDHGLANFDGTPLFHDPDPRRGWHQDWNSFIYDLGREQVRRFLVSNALYWFEQFHIDGIRVDAVASMLYLDYSRSHGQWIPNMDGGNENYDAIATLKWMNEEVYKYFPNAMTIAEESTAFPGVSAPTFMGGLGFGFKWNMGWMHDSLSYIKEEPVHRKYHHNTLTFPLVYAHSENYVLSLSHDEVVYGKGSIHNKMPGDEWQQTANLRAYFGYMYGQPGKKLNFMGAEIGQTAEWNHDDQLQWFLLDFPRHQGVQALTRDLNHLYRNEAALHDQDCIPAGFEWRLQDAAEQSIIAHERISEAGERILVVSNFTPVPRDEFRLGVPNKGRYQLLLNTDDSKYAGSGYEVVVDAKSEAVVSEDLAQSIVLRLPPLSTLFYKLV

Source

organism	Vibrio vulnificus MO6-24/O
ncbi_taxonomy_id	914127
host_organism	Escherichia coli BL21(DE3)

Entity 2 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	254

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6. Citations (1)

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length_a	166.800 Å
length_b	106.063 Å
length_c	141.126 Å
angle_alpha	90.00 °
angle_beta	123.30 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.500 Å
resolution_low	49.310 Å
r_factor	0.2169
r_work	0.2157
r_free	0.2567

fit	/app/data/saxs_computation/u7/9u77/9u77.fit
pddf	/app/data/pr_computation/u7/9u77/9u77.pr.out
profile	/app/data/saxs_computation/u7/9u77/9u77.dat

Crystal structure of Glycogen branching enzyme (VvGBE) from Vibrio vulnificus MO6-24/O

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)