SAXSdb — 1daa

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

D-AMINO ACID AMINOTRANSFERASE

Bacillus sp.

UniProt P19938

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 1–282 Chain B； UniProt 1–282	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.94 Å

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 1DAA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A0G L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE Deposited 1997-11-30	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 1–282（282 aa） Chain B 1–282（282 aa）	Mutation：L201A Mutation：L201A	PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；THE PROTEIN WAS PRE-INCUBATED WITH 50MM D-ALANINE AND 50MM ALPHA-KETOGLUTARATE TO CONVERT PLP INTO PMP. THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0	Resolution 2.00 Å R-free 0.263
2DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE Deposited 1997-10-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–282（282 aa） Chain B 1–282（282 aa）	Not recorded	DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22-26% PEG 4000, 0.2-0.3 M SODIUM ACETATE, 25 MM CYCLOSERINE AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.260
2DAB L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE Deposited 1997-11-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–282（282 aa） Chain B 1–282（282 aa）	Mutation：L201A Mutation：L201A	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0	Resolution 2.00 Å R-free 0.273
3DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE Deposited 1998-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–277（277 aa） Chain B 1–277（277 aa）	Not recorded	PDD N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PDA INACTIVATED PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 27% PEG 4000, 0.3 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.245
3LQS Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA) Deposited 2010-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–281（280 aa） Chain B 2–281（280 aa）	Not recorded	PSZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ratio of 200:1 prior to crystallization. The enzyme solution was mixed with crystallization buffer at pH 8.5 and incubated initially at 30-40 C, then allowed to return to room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.196
4DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM Deposited 1998-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–277（277 aa） Chain B 1–277（277 aa）	Not recorded	SO4 SULFATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 25% PEG 4000, 200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 1 MM ALPHA-KETOGLUTARATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop	Resolution 2.40 Å R-free 0.247
5DAA E177K MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE Deposited 1998-12-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–278（277 aa） Chain B 2–278（277 aa）	Mutation：E177K Mutation：E177K	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；PDA INACTIVATED PROTEIN WAS CONCENTRATED TO 30 MG/ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 27% PEG 4000, 0.4 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop	Resolution 2.90 Å R-free 0.245

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DAAA_BACYM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–282； UniProt 1–282 Author chain B； PDBConstruct 1–282； UniProt 1–282

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	1daa
Deposition date deposition_date	1995-06-09
Structure title title	CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE
Keywords keywords	TRANSFERASE, AMINOTRANSFERASE, D-AMINO ACID, D-ALANINE, PYRIDOXAL PHOSPHATE, TRANSFERASE (AMINOTRANSFERASE); TRANSFERASE (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	26.29 Å
Radius of gyration Rg (electron density) rg_electron	25.54 Å
Forward intensity I(0) i0	65583200.00
Molecular weight molecular_weight	63803.0 kDa
Excluded volume excluded_volume	80192 Å³
Envelope volume envelope_volume	95099 Å³
Hydration-shell volume shell_volume	30983 Å³
Envelope diameter envelope_diameter	86.6 Å
Shell Rg shell_rg	33.14 Å
Envelope Rg envelope_rg	25.77 Å
Shape Rg shape_rg	25.51 Å
Total Rg total_rg	26.44 Å
Total atoms total_atoms	4496
Residues n_residues	554
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	82.0 Å
Rg (real space) rg_real	26.27 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	6.5580e+07
I(0) uncertainty (real space) i0_real_error	1.0270e+06
Rg (reciprocal space) rg_reciprocal	26.28 Å
I(0) (reciprocal space) i0_reciprocal	65580000.0000
Solution quality estimate total_estimate	0.9026
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29150000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.958

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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	D-AMINO ACID AMINOTRANSFERASE
Molecular weight formula_weight	32311.9 kDa
EC 编号 ec_number	2.6.1.21
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	4728

GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPLHI

来源 Source

来源生物 organism	Bacillus sp.
NCBI Class编号 ncbi_taxonomy_id	72579

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1daaa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

Domain ID domain_id	d1daab_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

Domain ID domain_id	1daaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	1daaA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

Domain ID domain_id	1daaB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	1daaB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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8. Citations (3)

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Unit-cell length a length_a	58.500 Å
Unit-cell length b length_b	76.200 Å
Unit-cell length c length_c	73.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	—

fit	/app/data/saxs_computation/da/1daa/1daa.fit
pddf	/app/data/pr_computation/da/1daa/1daa.pr.out
profile	/app/data/saxs_computation/da/1daa/1daa.dat

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE

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

D-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