SAXSdb — 2ay3

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

AROMATIC AMINO ACID AMINOTRANSFERASE

Paracoccus denitrificans

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 1–394 Chain B； UniProt 1–394	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 MPP 3-(3,4-DIMETHOXYPHENYL)PROPIONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.7；pH 5.7	Resolution 2.40 Å R-free 0.221

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 2AY3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AY4 AROMATIC AMINO ACID AMINOTRANSFERASE WITHOUT SUBSTRATE Deposited 1997-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；PROTEIN WAS CRYSTALLIZED FROM 16.5% PEG 4000, 0.4 M SODIUM ACETATE, PH 5.7	Resolution 2.33 Å R-free 0.237
1AY5 AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH MALEATE Deposited 1997-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 MAE MALEIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 18.0% PEG 4000, 0.2 M SODIUM MALEATE, PH 5.6	Resolution 2.50 Å R-free 0.245
1AY8 AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH 3-PHENYLPROPIONATE Deposited 1997-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 HCI HYDROCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 18.0% PEG 4000, 0.2 M SODIUM MALEATE, PH 5.6; THEN SOAKED IN 20.0% PEG 4000, 0.2 M SODIUM CITRATE, 0.1 M 3-PHENYLPROPIONATE, PH 5.6	Resolution 2.30 Å R-free 0.239
2AY1 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 4-AMINOHYDROCINNAMIC ACID Deposited 1998-08-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 AHC 4-AMINOHYDROCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；pH 5.7	Resolution 2.20 Å R-free 0.240
2AY2 AROMATIC AMINO ACID AMINOTRANSFERASE WITH CYCLOHEXANE PROPIONIC ACID Deposited 1998-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 CXP CYCLOHEXANE PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.4	Resolution 2.40 Å R-free 0.234
2AY4 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(P-TOLYL)PROPIONIC ACID Deposited 1998-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 PPT 3-(P-TOLYL)PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；pH 6.2	Resolution 2.20 Å R-free 0.230
2AY5 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-INDOLEPROPIONIC ACID Deposited 1998-08-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 IOP INDOLYLPROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；pH 5.7	Resolution 2.40 Å R-free 0.218
2AY6 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-INDOLEBUTYRIC ACID Deposited 1998-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 3IB 3-INDOLEBUTYRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.20 Å R-free 0.258
2AY7 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 4-PHENYLBUTYRIC ACID Deposited 1998-08-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 CLT 4-PHENYL-BUTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；pH 5.7	Resolution 2.40 Å R-free 0.219
2AY8 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 4-(2-THIENYL)BUTYRIC ACID Deposited 1998-08-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 4TB 4-(2-THIENYL)BUTYRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；pH 5.7	Resolution 2.20 Å R-free 0.245
2AY9 AROMATIC AMINO ACID AMINOTRANSFERASE WITH 5-PHENYLVALERIC ACID Deposited 1998-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 5PV 5-PHENYLVALERIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.253

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TYRB_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394

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	2ay3
Deposition date deposition_date	1998-08-06
Structure title title	AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(3,4-DIMETHOXYPHENYL)PROPIONIC ACID
Keywords keywords	AMINOTRANSFERASE; AMINOTRANSFERASE
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	28.87 Å
Radius of gyration Rg (electron density) rg_electron	27.98 Å
Forward intensity I(0) i0	118776000.00
Molecular weight molecular_weight	85606.0 kDa
Excluded volume excluded_volume	106970 Å³
Envelope volume envelope_volume	127170 Å³
Hydration-shell volume shell_volume	37515 Å³
Envelope diameter envelope_diameter	104.6 Å
Shell Rg shell_rg	35.67 Å
Envelope Rg envelope_rg	28.30 Å
Shape Rg shape_rg	28.01 Å
Total Rg total_rg	28.58 Å
Total atoms total_atoms	6001
Residues n_residues	782
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	99.0 Å
Rg (real space) rg_real	28.89 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.1880e+08
I(0) uncertainty (real space) i0_real_error	1.9000e+06
Rg (reciprocal space) rg_reciprocal	28.88 Å
I(0) (reciprocal space) i0_reciprocal	118800000.0000
Solution quality estimate total_estimate	0.8676
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.120
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	59690000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.977

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	AROMATIC AMINO ACID AMINOTRANSFERASE
Molecular weight formula_weight	42780.0 kDa
EC 编号 ec_number	2.6.1.57
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	6325

MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEFGIYMVGDSRINIAGLNDNTIPILARAIIEVGV

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI Class编号 ncbi_taxonomy_id	266
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	3-(3,4-DIMETHOXYPHENYL)PROPIONIC ACID
Molecular weight formula_weight	210.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	324

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ay3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

Domain ID domain_id	d2ay3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

CATH v4.4 (4 domains)

Domain ID domain_id	2ay3A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2ay3A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2ay3B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2ay3B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (3)

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Unit-cell length a length_a	123.870 Å
Unit-cell length b length_b	121.690 Å
Unit-cell length c length_c	55.230 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	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	0.2210

fit	/app/data/saxs_computation/ay/2ay3/2ay3.fit
pddf	/app/data/pr_computation/ay/2ay3/2ay3.pr.out
profile	/app/data/saxs_computation/ay/2ay3/2ay3.dat

AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(3,4-DIMETHOXYPHENYL)PROPIONIC ACID

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

AROMATIC AMINO ACID AMINOTRANSFERASE

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