4f5g

Rational Design and Directed Evolution of E. coli Apartate Aminotransferase to Tyrosine Aminotransferase: Mutant P2.

Method: X-RAY DIFFRACTION Dmax: 95.7 Å Quality: GOOD

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 2–396 Chain B; UniProt 2–396 Mutation:I39V, N40D, I43V, N74T, I78L, I81L, T114S, S145A, V146I, I197A, F220I, F222I, A228G, Y254C, S283G, I351V Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;277 K;8% PEG 4000, 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.67 Å R-free 0.191

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 12–406; UniProt 2–396 Author chain B; PDBConstruct 12–406; UniProt 2–396

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 4f5g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f5g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f5g
Deposition date deposition_date2012-05-13
Structure title titleRational Design and Directed Evolution of E. coli Apartate Aminotransferase to Tyrosine Aminotransferase: Mutant P2.
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_guinier28.80
Radius of gyration Rg (electron density) rg_electron27.93
Forward intensity I(0) i0126485000.00
Molecular weight molecular_weight87547.0 kDa
Excluded volume excluded_volume108960 ų
Envelope volume envelope_volume129310 ų
Hydration-shell volume shell_volume38084 ų
Envelope diameter envelope_diameter98.9
Shell Rg shell_rg35.67
Envelope Rg envelope_rg28.03
Shape Rg shape_rg27.92
Total Rg total_rg28.64
Total atoms total_atoms6162
Residues n_residues796
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 dmax95.7
Rg (real space) rg_real28.76
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real1.2650e+08
I(0) uncertainty (real space) i0_real_error1.8150e+06
Rg (reciprocal space) rg_reciprocal28.78
I(0) (reciprocal space) i0_reciprocal126500000.0000
Solution quality estimate total_estimate0.8849
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41950000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4f5ga1
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
Domain ID domain_idd4f5ga2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4f5gb1
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
Domain ID domain_idd4f5gb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4f5gA01
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_id4f5gA02
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)
Domain ID domain_id4f5gB01
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_id4f5gB02
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)