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9qdh

Crystal structure of IgA protease (323-878) from Thomasclavelia ramosa

Method: X-RAY DIFFRACTION D_max: 88.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdh
deposition_date	2025-03-06
title	Crystal structure of IgA protease (323-878) from Thomasclavelia ramosa
keywords	;IgA protease, peptidase, protease, IgA-P, M64, metallopeptidase, metalloprotease, antibody, Ig, IgA, Thomasclavelia, metzincin, nephropathy, IgAN, hinge, 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	26.37 Å
rg_electron	25.41 Å
i0	67125000.00
molecular_weight	63345.0 kDa
excluded_volume	78789 Å³
envelope_volume	93060 Å³
shell_volume	30661 Å³
envelope_diameter	90.8 Å
shell_rg	32.68 Å
envelope_rg	25.51 Å
shape_rg	25.40 Å
total_rg	26.18 Å
total_atoms	4468
n_residues	554
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	88.4 Å
rg_real	26.38 Å
rg_real_error	0.63 Å
i0_real	6.7120e+07
i0_real_error	1.0850e+06
rg_reciprocal	26.38 Å
i0_reciprocal	67120000.0000
total_estimate	0.8794
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.404
kurtosis	-0.171
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	12730000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.959

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	IgA protease
formula_weight	63797.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4757

GGSGPDWNVSTEQSIQLTLGPWYSNDGKYSNPTIPVYTIQKTRSDTENMVVVVCGEGYTKSQQGKFINDVKRLWQDAMKYEPYRSYADRFNVYALCTASESTFDNGGSTFFDVIVDKYNSPVISNNLHGSQWKNHIFERCIGPEFIEKIHDAHIKKKCDPNTIPSGSEYEPYYYVHDYIAQFAMVVNTKSDFGGAYNNREYGFHYFISPSDSYRASKTFAHEFGHGLLGLGDEYSNGYLLDDKELKSLNLSSVEDPEKIKWRQLLGFRNTYTCRNAYGSKMLVSSYECIMRDTNYQFCEVCRLQGFKRMSQLVKDVDLYVATPEVKEYTGAYSKPSDFTDLETSSYYNYTYNRNDRLLSGNSKSRFNTNMNGKKIELRTVIQNISDKNARQLKFKMWIKHSDGSVATDSSGNPLQTVQTFDIPVWNDKANFWPLGALDHIKSDFNSGLKSCSLIYQIPSDAQLKSGDTVAFQVLDENGNVLADDNTETQRYTTVSIQYKFEDGSEIPNTAGGTFTVPYGTKLDLTPAKTLYDYEFIKVDGLNKPIVSDGTVVTYYYKNKN

Source

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

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	259

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6. Citations (1)

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length_a	70.739 Å
length_b	85.198 Å
length_c	90.666 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.000 Å
resolution_low	55.770 Å
r_factor	0.1965
r_work	0.1941
r_free	0.2448

fit	/app/data/saxs_computation/qd/9qdh/9qdh.fit
pddf	/app/data/pr_computation/qd/9qdh/9qdh.pr.out
profile	/app/data/saxs_computation/qd/9qdh/9qdh.dat

Crystal structure of IgA protease (323-878) from Thomasclavelia ramosa

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