SAXSdb — 9wzk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein disulfide isomerase-like 2-3

Oryza sativa subsp. japonica

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 149–441 Chain B； UniProt 149–441	Mutation：C195A, C198A	BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, pH 5.5	Resolution 1.80 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9WZK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9WZL Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain Deposited 2025-09-29	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 149–441（293 aa） Chain B 149–441（293 aa）	Not recorded	BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, pH 5.5	Resolution 2.10 Å R-free 0.253
9WZM Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a0 domain Deposited 2025-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–170（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2M ammonium sulfate, 0.2M lithium sulfate, 0.2M diammonium phosphate	Resolution 2.10 Å R-free 0.222

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDI23_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–296； UniProt 149–441 Author chain B； PDBConstruct 4–296； UniProt 149–441

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9wzk
Deposition date deposition_date	2025-09-29
Structure title title	Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains
Keywords keywords	endosperm, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	41.83 Å
Radius of gyration Rg (electron density) rg_electron	42.49 Å
Forward intensity I(0) i0	44624700.00
Molecular weight molecular_weight	55483.0 kDa
Excluded volume excluded_volume	70168 Å³
Envelope volume envelope_volume	103840 Å³
Hydration-shell volume shell_volume	24161 Å³
Envelope diameter envelope_diameter	140.6 Å
Shell Rg shell_rg	38.79 Å
Envelope Rg envelope_rg	42.14 Å
Shape Rg shape_rg	42.47 Å
Total Rg total_rg	42.33 Å
Total atoms total_atoms	3916
Residues n_residues	508
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	132.9 Å
Rg (real space) rg_real	42.59 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	4.4620e+07
I(0) uncertainty (real space) i0_real_error	7.7760e+05
Rg (reciprocal space) rg_reciprocal	41.83 Å
I(0) (reciprocal space) i0_reciprocal	44590000.0000
Solution quality estimate total_estimate	0.6191
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.567
Kurtosis Kurtosis kurtosis	-0.634
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1693000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein disulfide isomerase-like 2-3
Molecular weight formula_weight	31980.0 kDa
EC 编号 ec_number	5.3.4.1
Mutation mutation	C195A, C198A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4157

GPLGSGGKKSGGSSEKTEPSASIELNSQNFDKLVTKSKDLWIVEFFAPWAGHAKKLAPEWKKAAKNLKGQVKLGHVDCDAEKSLMSKYKVEGFPTILVFGADKESPFPYQGARVASAIESFALEQLEANAAPPEVSELTGPDAMEEKCASAAICFVSFLPDILDSKAEGRNKYLELLLSVAEKFKKSPYSFVWTAAGKQADLEKQVGVGGYGYPAMVALNVKKGAYAPLRSAFQLDEITEFVREAGRGGKGNLPLDGTPTIVQSEPWDGKDGEVIEEDEFSLEELMADNSPVNDEL

来源 Source

来源生物 organism	Oryza sativa subsp. japonica
通用名 common_name	Japanese rice
NCBI Class编号 ncbi_taxonomy_id	39947
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

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8. Citations (1)

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Unit-cell length a length_a	35.169 Å
Unit-cell length b length_b	171.462 Å
Unit-cell length c length_c	52.726 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	28.330 Å
R factor r_factor	—
R_work r_work	0.2213
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein disulfide isomerase-like 2-3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction