SAXSdb — 4r4y

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

N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase

Elizabethkingia miricola

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 46–340 Chain B； UniProt 46–340	Fragment：UNP residues 46-340 Mutation：G172D	SD4 N-hydroxy-L-asparagine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；298 K；0.2M NaCl, 0.1M Bis-Tris pH 6.5, 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.10 Å R-free 0.252

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 4R4Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AYY GLYCOSYLASPARAGINASE Deposited 1997-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 46–196（151 aa） Chain B 197–340（144 aa） Chain C 46–196（151 aa） Chain D 197–340（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；19% PEG3350 IN 100 MM TRIS.HCL PH 8.5	Resolution 2.32 Å R-free 0.270
1P4K CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT Deposited 2003-04-23	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 46–340（295 aa） Fragment：Glycosylasparaginase, alpha and beta chains Chain C 46–340（295 aa） Fragment：Glycosylasparaginase, alpha and beta chains	Mutation：D151N Mutation：D151N	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；15% PEG 3300, 0.1M Tris, pH 7.5, 0.2M lithium sulfate, 0.1% sodium azide, EVAPORATION	Resolution 1.90 Å R-free 0.220
1P4V CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT WITH GLYCINE Deposited 2003-04-24	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 46–340（295 aa） Fragment：Glycosylasparaginase, alpha and beta chains Chain C 46–340（295 aa） Fragment：Glycosylasparaginase, alpha and beta chains	Mutation：D151N Mutation：D151N	GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；15% PEG 3300, 0.1M Tris, pH 7.5, 0.2M lithium sulfate, 0.1% sodium azide, 0.05M glycine, EVAPORATION	Resolution 1.90 Å R-free 0.225
2GAC T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1998-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 46–196（151 aa） Chain B 198–340（143 aa） Chain C 46–196（151 aa） Chain D 198–340（143 aa）	Mutation：T152C Mutation：T152C Mutation：T152C Mutation：T152C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.10 Å R-free 0.280
2GAW WILD TYPE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1998-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 46–196（151 aa） Chain B 197–340（144 aa） Chain C 46–196（151 aa） Chain D 197–340（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.20 Å R-free 0.297
2GL9 Crystal Structure of Glycosylasparaginase-Substrate Complex Deposited 2006-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 46–196（151 aa） Fragment：residues 46-196 Chain B 197–340（144 aa） Fragment：residues 197-340 Chain C 46–196（151 aa） Fragment：residues 46-196 Chain D 197–340（144 aa） Fragment：residues 197-340	Mutation：T152C Mutation：T152C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ASN ASPARAGINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；15% PEG 3350, 100 mM HEPES, 0.1% sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.215
3LJQ Crystal Structure of the Glycosylasparaginase T152C apo-precursor Deposited 2010-01-26	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 46–340（295 aa） Fragment：UNP residues 46-340 Chain C 46–340（295 aa） Fragment：UNP residues 46-340	Mutation：T152C Mutation：T152C	NA SODIUM ION × 2 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；277 K；15% PEG 3350, 100 mM HEPES pH 7.5, 0.1% sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.197
9GAA PRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1999-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 46–340（295 aa）	Mutation：T152A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE	Resolution 2.10 Å R-free 0.297
9GAA PRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1999-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 46–340（295 aa）	Mutation：T152A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE	Resolution 2.10 Å R-free 0.297
9GAA PRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1999-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 46–340（295 aa） Chain C 46–340（295 aa）	Mutation：T152A Mutation：T152A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE	Resolution 2.10 Å R-free 0.297
9GAC PRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1999-06-15	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 46–340（295 aa） Chain C 46–340（295 aa）	Mutation：T152C Mutation：T152C	GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE	Resolution 1.90 Å R-free 0.278
9GAF PRECURSOR OF THE W11F MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM Deposited 1999-06-15	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 47–340（294 aa） Chain C 47–340（294 aa）	Mutation：W11F Mutation：W11F	GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 3300, 100MM TRIS, PH 7.5, 0.2M LITHIUM SULFATE, 0.1% SODIUM AZIDE	Resolution 1.90 Å R-free 0.239

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ASPG_ELIMR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 46–340 Author chain B； PDBConstruct 1–295； UniProt 46–340

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	4r4y
Deposition date deposition_date	2014-08-20
Structure title title	Structural basis of a point mutation that causes the genetic disease Aspartylglucosaminuria
Keywords keywords	AGU structure, autoprocessing, glycosylasparaginase, lysosomal storage disease, pre-autoproteolysis trap, 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	23.44 Å
Radius of gyration Rg (electron density) rg_electron	22.53 Å
Forward intensity I(0) i0	64550700.00
Molecular weight molecular_weight	61674.0 kDa
Excluded volume excluded_volume	76798 Å³
Envelope volume envelope_volume	86398 Å³
Hydration-shell volume shell_volume	30548 Å³
Envelope diameter envelope_diameter	75.7 Å
Shell Rg shell_rg	30.91 Å
Envelope Rg envelope_rg	22.91 Å
Shape Rg shape_rg	22.55 Å
Total Rg total_rg	23.34 Å
Total atoms total_atoms	4326
Residues n_residues	564
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	72.6 Å
Rg (real space) rg_real	23.28 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	6.4550e+07
I(0) uncertainty (real space) i0_real_error	8.9140e+05
Rg (reciprocal space) rg_reciprocal	23.32 Å
I(0) (reciprocal space) i0_reciprocal	64550000.0000
Solution quality estimate total_estimate	0.9001
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27050000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.999

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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	N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase
Molecular weight formula_weight	32237.7 kDa
EC 编号 ec_number	3.5.1.26
Mutation mutation	G172D
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	4413

TTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHDTIGMIALDAQGNLSGACTTSDMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK

来源 Source

来源生物 organism	Elizabethkingia miricola
NCBI Class编号 ncbi_taxonomy_id	172045
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-hydroxy-L-asparagine
Molecular weight formula_weight	148.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4r4ya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.5 — (Glycosyl)asparaginase

Domain ID domain_id	d4r4yb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.5 — (Glycosyl)asparaginase

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8. Citations (1)

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Unit-cell length a length_a	45.810 Å
Unit-cell length b length_b	50.620 Å
Unit-cell length c length_c	61.230 Å
Unit-cell angle α angle_alpha	86.28 °
Unit-cell angle β angle_beta	91.04 °
Unit-cell angle γ angle_gamma	107.75 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	39.000 Å
R factor r_factor	0.1940
R_work r_work	0.1900
R_free r_free	0.2520

fit	/app/data/saxs_computation/r4/4r4y/4r4y.fit
pddf	/app/data/pr_computation/r4/4r4y/4r4y.pr.out
profile	/app/data/saxs_computation/r4/4r4y/4r4y.dat

Structural basis of a point mutation that causes the genetic disease Aspartylglucosaminuria

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

N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase

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