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9wzk

Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains

Method: X-RAY DIFFRACTION D_max: 132.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wzk
deposition_date	2025-09-29
title	Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains
keywords	endosperm, PLANT PROTEIN; PLANT PROTEIN
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	41.83 Å
rg_electron	42.49 Å
i0	44624700.00
molecular_weight	55483.0 kDa
excluded_volume	70168 Å³
envelope_volume	103840 Å³
shell_volume	24161 Å³
envelope_diameter	140.6 Å
shell_rg	38.79 Å
envelope_rg	42.14 Å
shape_rg	42.47 Å
total_rg	42.33 Å
total_atoms	3916
n_residues	508
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	132.9 Å
rg_real	42.59 Å
rg_real_error	1.61 Å
i0_real	4.4620e+07
i0_real_error	7.7760e+05
rg_reciprocal	41.83 Å
i0_reciprocal	44590000.0000
total_estimate	0.6191
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	21.0 Å
skewness	0.567
kurtosis	-0.634
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	1693000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.297; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.158; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Protein disulfide isomerase-like 2-3
formula_weight	31980.0 kDa
ec_number	5.3.4.1
mutation	C195A, C198A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4157

GPLGSGGKKSGGSSEKTEPSASIELNSQNFDKLVTKSKDLWIVEFFAPWAGHAKKLAPEWKKAAKNLKGQVKLGHVDCDAEKSLMSKYKVEGFPTILVFGADKESPFPYQGARVASAIESFALEQLEANAAPPEVSELTGPDAMEEKCASAAICFVSFLPDILDSKAEGRNKYLELLLSVAEKFKKSPYSFVWTAAGKQADLEKQVGVGGYGYPAMVALNVKKGAYAPLRSAFQLDEITEFVREAGRGGKGNLPLDGTPTIVQSEPWDGKDGEVIEEDEFSLEELMADNSPVNDEL

Source

organism	Oryza sativa subsp. japonica
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	209.2 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	235

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6. Citations (1)

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length_a	35.169 Å
length_b	171.462 Å
length_c	52.726 Å
angle_alpha	90.00 °
angle_beta	106.27 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	28.330 Å
r_factor	—
r_work	0.2213
r_free	0.2655

fit	/app/data/saxs_computation/wz/9wzk/9wzk.fit
pddf	/app/data/pr_computation/wz/9wzk/9wzk.pr.out
profile	/app/data/saxs_computation/wz/9wzk/9wzk.dat

Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains

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