Structure of the GH13 domain of Ruminococcus bromii Amy4

Method: ELECTRON MICROSCOPY D_max: 83.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qf3
deposition_date	2025-03-11
title	Structure of the GH13 domain of Ruminococcus bromii Amy4
keywords	GH13, Ruminococcus bromii, Amy4, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	24.53 Å
rg_electron	23.61 Å
i0	68093900.00
molecular_weight	62761.0 kDa
excluded_volume	77352 Å³
envelope_volume	84685 Å³
shell_volume	29541 Å³
envelope_diameter	87.3 Å
shell_rg	31.46 Å
envelope_rg	24.04 Å
shape_rg	23.57 Å
total_rg	24.51 Å
total_atoms	8540
n_residues	570
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	83.2 Å
rg_real	24.52 Å
rg_real_error	0.47 Å
i0_real	6.8090e+07
i0_real_error	9.2150e+05
rg_reciprocal	24.52 Å
i0_reciprocal	68090000.0000
total_estimate	0.8684
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.418
kurtosis	-0.089
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	16440000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Ruminococcus bromii Amy4
formula_weight	135746.0 kDa
ec_number	3.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8540

MGATVSDDSSTSASSTAAGSLVEDDGFTWDNANVYFLLTDRFKNGNTANDHSYGRTLDKDGKPLEGWDTNPGTFHGGDFAGVTQSIEEGYFDNLGVNAIWISAPYEQTHGYCDSGKGFAHYSYHGYYVLDYTETDANFGTKEEFKTLVDTAHEHGIRVIMDIVMNHTGYNTVADMEQFGFGTLLDGALDFKYKLTDVGEVNDHIDYKTSEEDWGKWWSNDWIRSGLPGYTEGAGGDLTMSLSGLPDFRTEQTKDVTIPPILKTKWTQEGTYAQKLAKYGDKNTVTGYLSTWLSEWVREYGVDGFRCDTAKHVDKASWNQLKQACVSALREWRSNNKGKAGADWKEDFWMTGEHWDHGVGYDTYYSEGGFDSMINFAVTGGGALASGSVANTYQGYADKINTKEGFNVLSFMSSHDETLTRGDENTMLYNAAAFLLLPGGVQIFYGDETNRPLYPGVAFDGYGGSGHALRSDMNWNDMDKTLLAQWQKVGQFRNKHVSIGAGANVKLSATSGVAFGRTYDKNGVTDQAAAVIGCNKNSSVTVDVSTLWEDGSYVINTYDNSSSVVTDGKVTFNSGVNGTILMENADGQPLVSITGEPKFYGTEQVTVSLKECDSAKVSVDGGNKFVVKDGDTFTIGQTAYKNDTIEVTVEATNDKASSEAKFTFLKLGENDEKPTTSPTQSTTVPGSTASQTSKLTIKSTAGAPNVYAWTGASTALNGAWPGQKAAAVSGQANTYELTLPVSADKSFSVVLNNGSGSQSGDITGLYDGAVLEIQNGNYASVKTVTNGNQQGGGGEPEPAEGSVSVTIKPYSPSASYKIYAWNDTQKLTGAWPGVALTEKDSDGNYVVKFDNVDEVSIILSSGSGQTADITGVRDGATIEITNEGCTTYKLTSKPIVVSPYESLKKEARKILAMTASDYTAESWANAQKVLKSAEAMIKAGEDATTAEDMNAMIADLKSAQKALVLAPATLTYAVVGKSVVSGVTASAAKVTVTVDGKTYTATADDVTGAFTVATSALKGTSTIKVDATRNGVNGTYSYAMKNGNIENGFVPTSPTLPTQPTTSTQPTTATQPTTATQPTAPTQPTTATEPTTAPAQKLTVNATSNYFGSASKTVSTDGKKVTVLYKLNSNMGVVDGQWAVKYDSSKLKFNMADNKADGKQTIMPSQSNLIHNAYSNVIKGVFTNPQVPTQYNGDTFISLTFEVIGSGTASVYLDTQYLTLGYVKGNKLNQASVVNNSKVCDVTGIAGFEKVSVNASTAFVGDVTHHHHHH

Source

organism	Ruminococcus bromii L2-63
ncbi_taxonomy_id	657321
host_organism	Escherichia coli BL21(DE3)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.80 Å
resolution_method	—
num_particles	905000

fit	/app/data/saxs_computation/qf/9qf3/9qf3.fit
pddf	/app/data/pr_computation/qf/9qf3/9qf3.pr.out
profile	/app/data/saxs_computation/qf/9qf3/9qf3.dat

Structure of the GH13 domain of Ruminococcus bromii Amy4

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

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)