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9wzl

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

Method: X-RAY DIFFRACTION Dmax: 134.5 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein disulfide isomerase-like 2-3

Oryza sativa Japonica Group

UniProt Q67UF5

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 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

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 9WZL 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 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）
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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 9wzl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9wzl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9wzl
Deposition date deposition_date2025-09-29
Structure title titleCrystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain
Keywords keywordsendosperm, PLANT PROTEIN; PLANT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.73 Å
Radius of gyration Rg (electron density) rg_electron42.49 Å
Forward intensity I(0) i045394800.00
Molecular weight molecular_weight55981.0 kDa
Excluded volume excluded_volume70756 ų
Envelope volume envelope_volume103340 ų
Hydration-shell volume shell_volume23761 ų
Envelope diameter envelope_diameter146.7 Å
Shell Rg shell_rg39.16 Å
Envelope Rg envelope_rg42.29 Å
Shape Rg shape_rg42.49 Å
Total Rg total_rg42.30 Å
Total atoms total_atoms3946
Residues n_residues511
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax134.5 Å
Rg (real space) rg_real42.47 Å
Rg uncertainty (real space) rg_real_error1.82 Å
I(0) (real space) i0_real4.5390e+07
I(0) uncertainty (real space) i0_real_error9.1930e+05
Rg (reciprocal space) rg_reciprocal41.74 Å
I(0) (reciprocal space) i0_reciprocal45360000.0000
Solution quality estimate total_estimate0.3910
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2 Å
Skewness Skewness skewness0.557
Kurtosis Kurtosis kurtosis-0.646
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1722000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.268; Stabil: 0.999; Sysdev: 0.046; Positv: 1.000; Valcen: 0.139; 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)

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8. Citations (1)

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9. Files and Curves (10)