Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy12

Method: ELECTRON MICROSCOPY D_max: 97.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qfa
deposition_date	2025-03-11
title	Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy12
keywords	GH13, Ruminococcus bromii, Amy12, MucBP, 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	28.45 Å
rg_electron	27.90 Å
i0	117268000.00
molecular_weight	83401.0 kDa
excluded_volume	103050 Å³
envelope_volume	121780 Å³
shell_volume	36200 Å³
envelope_diameter	101.2 Å
shell_rg	35.65 Å
envelope_rg	28.38 Å
shape_rg	27.90 Å
total_rg	28.56 Å
total_atoms	11416
n_residues	760
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	97.5 Å
rg_real	28.49 Å
rg_real_error	0.65 Å
i0_real	1.1730e+08
i0_real_error	1.7490e+06
rg_reciprocal	28.48 Å
i0_reciprocal	117300000.0000
total_estimate	0.8654
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.1 Å
skewness	0.438
kurtosis	-0.203
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0001
highest_alpha	27060000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Ruminococcus bromii Amy12
formula_weight	114603.8 kDa
ec_number	3.2.1.41
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11416

MAHHHHHHATADDSSAVSSDYARDNSYTKAAEDIDAQYAYSGNDLGVTYTKDATTFKVWSPTATGVKLNIFTKGSDDEQGASKVASYTLEKMLVDGEWNGVWTITLVGEWKDYYYTYSVTTTDTTHIGSDATKTYETQDVYSTATGVNGKRSMIVDLDETDPEGWSNDSHVLLDKSTKSSVWELHIKDFSYDKASGVSDANRGKYLAFTENGTTLNGEGKVSTCIDYLKELGVTTVQLNPFYDFQSVNEAGDDSQFNWGYDPVNYNVPEGSYSSNPYDGKVRIKECKEMIKALHDAGISVVMDVVYNHTYSTDSCFQYTVPNYYYRMKTTGAFSDGSGCGNEGATERAMYRQYVIDSLKYWVNEYHVDGFRFDLMGLMDVETMNMAREALDQIDPRITMWGEGWAGGDSYHPTNTCSGTKFYPATQANASRLSDRIAIFNDGIRDGIKGSAMDISDVGFIQGSKSSAKGVSYGVRANSSGTYKWKAQAPSQCVTYDACHDNATLYDQIIASTGLADYGERNSEAVKMNRLASAIIYTSQGISFTLAGEEMARSKDGDTNSYKSAANLNMIKWQNVVDYADVVSYYKGMMQIKSAFSPLTAMDNSYADKYTFTKKVSASTNQISFTIQNDVEGEWNKMAVIYNNATTAADVTLSDTSVTDWVVIANGETAGLDSLGEVTGSTFTVPARSAIVAVDKAGYESAGIHSSKGKVKVNYVYEATGEKLEDSVILQGSVGSGYVTVPSAVIPDTYIVSRIGGNAEGKYTSDMQEVTYYYTDYIPESLKNADFNGDGEINVIDATLLQKYIAKLETPTVDESTLDLNYDGTFNIEDSTMIMKYVARIPVSSGKVTVNYYYTDADGKQQKLTDSIVFAGRAGSTYKSTAFKVVGYAVDPDRMPENQSGLIPYGEAEVNYYYIASSLDIKLHVKHNGSLTWTPYLWIWGSDLKGKDSGNFMSEWPGDPMTEGENGWFDYSFTYKGAGTYNVIVSDNATNQTIDYKGFVDNEMWIVIDDSAVMGSTYLTFYTDNPDTNPNAPIAEQVTLG

Source

organism	Ruminococcus bromii L2-63
ncbi_taxonomy_id	657321
host_organism	Escherichia coli

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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	3.10 Å
resolution_method	—
num_particles	199170

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

Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy12

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)