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4daa

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD
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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 1–277 Chain B； UniProt 1–277 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

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 4DAA 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 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 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
1DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE Deposited 1995-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–282（282 aa）
Chain B 1–282（282 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.94 Å
2DAA CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE Deposited 1997-10-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–282（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 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 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 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
5DAA E177K MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE Deposited 1998-12-13 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 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 1–277； UniProt 1–277 Author chain B； PDBConstruct 1–277； UniProt 1–277

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 4daa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4daa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4daa
Deposition date deposition_date1998-01-26
Structure title titleCRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM
Keywords keywordsAMINOTRANSFERASE, PYRIDOXAL PHOSPHATE, TRANSAMINASE; AMINOTRANSFERASE
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_guinier26.11 Å
Radius of gyration Rg (electron density) rg_electron25.41 Å
Forward intensity I(0) i066563200.00
Molecular weight molecular_weight63997.0 kDa
Excluded volume excluded_volume80316 ų
Envelope volume envelope_volume94175 ų
Hydration-shell volume shell_volume30850 ų
Envelope diameter envelope_diameter84.5 Å
Shell Rg shell_rg32.93 Å
Envelope Rg envelope_rg25.60 Å
Shape Rg shape_rg25.39 Å
Total Rg total_rg26.29 Å
Total atoms total_atoms4506
Residues n_residues554
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 dmax82.2 Å
Rg (real space) rg_real26.09 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real6.6560e+07
I(0) uncertainty (real space) i0_real_error8.4630e+05
Rg (reciprocal space) rg_reciprocal26.10 Å
I(0) (reciprocal space) i0_reciprocal66560000.0000
Solution quality estimate total_estimate0.8983
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.391
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32570000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.924
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4daaa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamilye.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family familye.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Domain ID domain_idd4daab_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamilye.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family familye.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

Domain ID domain_id4daaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain
Domain ID domain_id4daaA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-amino Acid Aminotransferase, subunit A, domain 2
Domain ID domain_id4daaB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain
Domain ID domain_id4daaB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-amino Acid Aminotransferase, subunit A, domain 2
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8. Citations (2)

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9. Files and Curves (10)