3qn6

Crystal Structures of Escherichia coli Aspartate Aminotransferase Reconstituted with 1-Deaza-Pyridoxal 5'-Phosphate: Internal Aldimine and Stable L-Aspartate External Aldimine

Method: X-RAY DIFFRACTION Dmax: 68.2 Å Quality: EXCELLENT

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

Aspartate aminotransferase

Escherichia coli

UniProt P00509

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 1–396 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;2 L of protein (15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 M deaza-PLP) mixed with 2 L reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA, pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.79 Å R-free 0.188

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.

103 other PDB entries and 104 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AAT_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–396; UniProt 1–396

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 3qn6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qn6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qn6
Deposition date deposition_date2011-02-08
Structure title titleCrystal Structures of Escherichia coli Aspartate Aminotransferase Reconstituted with 1-Deaza-Pyridoxal 5'-Phosphate: Internal Aldimine and Stable L-Aspartate External Aldimine
Keywords keywordsAminotransferase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.74
Radius of gyration Rg (electron density) rg_electron21.54
Forward intensity I(0) i034777600.00
Molecular weight molecular_weight44118.0 kDa
Excluded volume excluded_volume54678 ų
Envelope volume envelope_volume66330 ų
Hydration-shell volume shell_volume25207 ų
Envelope diameter envelope_diameter69.8
Shell Rg shell_rg28.81
Envelope Rg envelope_rg21.91
Shape Rg shape_rg21.50
Total Rg total_rg22.52
Total atoms total_atoms3097
Residues n_residues394
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.2
Rg (real space) rg_real22.64
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real3.4780e+07
I(0) uncertainty (real space) i0_real_error4.2580e+05
Rg (reciprocal space) rg_reciprocal22.66
I(0) (reciprocal space) i0_reciprocal34780000.0000
Solution quality estimate total_estimate0.9116
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.185
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7491000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3qn6a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.1 — AAT-like

CATH v4.4 (2 domains)

Domain ID domain_id3qn6A01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id3qn6A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

8. Citations (1)

9. Files and Curves (10)