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9qa6

Cryo-EM structure of Thomasclavelia ramosa IgA peptidase (IgAse) active site mutant (S32-N876)

Method: ELECTRON MICROSCOPY D_max: 100.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qa6
deposition_date	2025-02-27
title	Cryo-EM structure of Thomasclavelia ramosa IgA peptidase (IgAse) active site mutant (S32-N876)
keywords	Protease, Metallopeptidase, Metzincin, 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	32.27 Å
rg_electron	31.68 Å
i0	153484000.00
molecular_weight	96222.0 kDa
excluded_volume	119000 Å³
envelope_volume	147890 Å³
shell_volume	38552 Å³
envelope_diameter	106.2 Å
shell_rg	38.70 Å
envelope_rg	31.53 Å
shape_rg	31.68 Å
total_rg	32.26 Å
total_atoms	6780
n_residues	844
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	100.8 Å
rg_real	32.22 Å
rg_real_error	0.55 Å
i0_real	1.5350e+08
i0_real_error	2.1110e+06
rg_reciprocal	32.25 Å
i0_reciprocal	153500000.0000
total_estimate	0.9061
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	32.9 Å
skewness	0.213
kurtosis	-0.659
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	25290000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.906

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	IgA protease
formula_weight	128082.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7043

MASKPDIKVGDYVKMGVYNNASILWRCVSIDNNGPLMLADKIVDTLAYDAKTNDNSNSKSHSRSYKRDDYGSNYWKDSNMRSWLNSTAAEGKVDWLCGNPPKDGYVSGVGAYNEKAGFLNAFSKSEIAAMKTVTQRSLVSHPEYNKGIVDGDANSDLLYYTDISEAVANYDSSYFETTTEKVFLLDVKQANAVWKNLKGYYVAYNNDGMAWPYWLRTPVTDCNHDMRYISSSGQVGRYAPWYSDLGVRPAFYLDSEYFVTTSGSGSQSSPYIGSAPNKQEDDYTISEPAEDANPDWNVSTEQSIQLTLGPWYSNDGKYSNPTIPVYTIQKTRSDTENMVVVVCGEGYTKSQQGKFINDVKRLWQDAMKYEPYRSYADRFNVYALCTASESTFDNGGSTFFDVIVDKYNSPVISNNLHGSQWKNHIFERCIGPEFIEKIHDAHIKKKCDPNTIPSGSEYEPYYYVHDYIAQFAMVVNTKSDFGGAYNNREYGFHYFISPSDSYRASKTFAHAFGHGLLGLGDEYSNGYLLDDKELKSLNLSSVEDPEKIKWRQLLGFRNTYTCRNAYGSKMLVSSYECIMRDTNYQFCEVCRLQGFKRMSQLVKDVDLYVATPEVKEYTGAYSKPSDFTDLETSSYYNYTYNRNDRLLSGNSKSRFNTNMNGKKIELRTVIQNISDKNARQLKFKMWIKHSDGSVATDSSGNPLQTVQTFDIPVWNDKANFWPLGALDHIKSDFNSGLKSCSLIYQIPSDAQLKSGDTVAFQVLDENGNVLADDNTETQRYTTVSIQYKFEDGSEIPNTAGGTFTVPYGTKLDLTPAKTLYDYEFIKVDGLNKPIVSDGTVVTYYYKNKNEEHTHNLTLVAAKAATCTTAGNSAYYTCDGCDKWFADATGSVEITDKTSVKIPAPGHTAGTEWKSDDTNHWHECTVAGCGVIIESTKSAHTAGEWIVDTPATATTAGTKHKECTVCHRVLETQPIPSTGTELKIIAGDNQIYNKASGSDVTITCNGDFAKFTGIKVDGSVVDSSNYTAVSGSTVLTLKASYLGTLTDGSHTITFVYTDGEANANLTVRTAGSGHIHDYGTEWKSNADNHWHECNCGDKKDEAAHSFKWVVDKEATATKKGSKHEECKICGYKRSAVEILEHHHHHH

Source

organism	Thomasclavelia ramosa
ncbi_taxonomy_id	1547
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	AZIDE ION
formula_weight	42.0 kDa
src_method	syn
entity_count	7

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	151

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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	—

resolution	2.81 Å
resolution_method	—
num_particles	312476

fit	/app/data/saxs_computation/qa/9qa6/9qa6.fit
pddf	/app/data/pr_computation/qa/9qa6/9qa6.pr.out
profile	/app/data/saxs_computation/qa/9qa6/9qa6.dat