SAXSdb — 9ykf

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

Protein/nucleic acid deglycase 3

Escherichia coli

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 1–196 Chain B； UniProt 1–196	Mutation：D23N	EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 5 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；22-25% PEG 4000, 200 mM MgCl2, and 100 mM Tris, pH=8.5	Resolution 0.98 Å R-free 0.114

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 9YKF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AB0 Crystal Structure of E. coli protein YajL (ThiJ) Deposited 2005-07-14	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 1–196（196 aa） Chain B 1–196（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG4000, Tris-HCl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.10 Å R-free 0.171

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YAJL_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–199； UniProt 1–196 Author chain B； PDBConstruct 4–199； UniProt 1–196

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	9ykf
Deposition date deposition_date	2025-10-07
Structure title title	Crystal Structure of E. coli D23N YajL
Keywords keywords	DJ-1 superfamily, Cysteine dependent enzyme, HYDROLASE; HYDROLASE
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	21.86 Å
Radius of gyration Rg (electron density) rg_electron	20.73 Å
Forward intensity I(0) i0	27947000.00
Molecular weight molecular_weight	41658.0 kDa
Excluded volume excluded_volume	52698 Å³
Envelope volume envelope_volume	59342 Å³
Hydration-shell volume shell_volume	23585 Å³
Envelope diameter envelope_diameter	69.5 Å
Shell Rg shell_rg	27.65 Å
Envelope Rg envelope_rg	21.04 Å
Shape Rg shape_rg	20.75 Å
Total Rg total_rg	21.57 Å
Total atoms total_atoms	5915
Residues n_residues	389
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	68.8 Å
Rg (real space) rg_real	21.79 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.7950e+07
I(0) uncertainty (real space) i0_real_error	3.1460e+05
Rg (reciprocal space) rg_reciprocal	21.80 Å
I(0) (reciprocal space) i0_reciprocal	27950000.0000
Solution quality estimate total_estimate	0.7458
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.297
Kurtosis Kurtosis kurtosis	-0.331
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6952000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 0.348; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein/nucleic acid deglycase 3
Molecular weight formula_weight	21079.3 kDa
EC 编号 ec_number	3.1.2.-,3.5.1.-,3.5.1.124
Mutation mutation	D23N
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	8008

GSHMSASALVCLAPGSEETEAVTTINLLVRGGIKVTTASVASDGNLAITCSRGVKLLADAPLVEVADGEYDVIVLPGGIKGAECFRDSTLLVETVKQFHRSGRIVAAICAAPATVLVPHDIFPIGNMTGFPTLKDKIPAEQWLDKRVVWDARVKLLTSQGPGTAIDFGLKIIDLLVGREKAHEVASQLVMAAGIYNYYE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	576

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8. Citations (2)

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Unit-cell length a length_a	43.723 Å
Unit-cell length b length_b	78.335 Å
Unit-cell length c length_c	99.614 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	0.980 Å
Low-resolution limit resolution_low	39.170 Å
R factor r_factor	0.0974
R_work r_work	0.0969
R_free r_free	0.1144

fit	/app/data/saxs_computation/yk/9ykf/9ykf.fit
pddf	/app/data/pr_computation/yk/9ykf/9ykf.pr.out
profile	/app/data/saxs_computation/yk/9ykf/9ykf.dat

Crystal Structure of E. coli D23N YajL

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

Protein/nucleic acid deglycase 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