SAXSdb — 9wzm

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

Protein disulfide isomerase-like 2-3

Oryza sativa Japonica Group

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 27–170	Not recorded	No other associated polymer	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

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 9WZM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9WZK Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains 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 149–441（293 aa） Chain B 149–441（293 aa）	Mutation：C195A, C198A 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
9WZL Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b 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 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

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 2–145； UniProt 27–170

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	9wzm
Deposition date deposition_date	2025-09-29
Structure title title	Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a0 domain
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	15.49 Å
Radius of gyration Rg (electron density) rg_electron	14.05 Å
Forward intensity I(0) i0	3116130.00
Molecular weight molecular_weight	12961.0 kDa
Excluded volume excluded_volume	16513 Å³
Envelope volume envelope_volume	18486 Å³
Hydration-shell volume shell_volume	11508 Å³
Envelope diameter envelope_diameter	48.7 Å
Shell Rg shell_rg	19.43 Å
Envelope Rg envelope_rg	14.33 Å
Shape Rg shape_rg	14.01 Å
Total Rg total_rg	15.33 Å
Total atoms total_atoms	917
Residues n_residues	119
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	50.7 Å
Rg (real space) rg_real	15.43 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	3.1160e+06
I(0) uncertainty (real space) i0_real_error	3.2460e+04
Rg (reciprocal space) rg_reciprocal	15.43 Å
I(0) (reciprocal space) i0_reciprocal	3116000.0000
Solution quality estimate total_estimate	0.8777
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.207
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	515600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	61.773 Å
Unit-cell length b length_b	61.773 Å
Unit-cell length c length_c	100.761 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.906 Å
R factor r_factor	—
R_work r_work	0.1944
R_free r_free	0.2221

Description description	Protein disulfide isomerase-like 2-3
Molecular weight formula_weight	16356.6 kDa
EC 编号 ec_number	5.3.4.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	976

Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a0 domain

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Oryza sativa Japonica Group
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)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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