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1eov

FREE ASPARTYL-TRNA SYNTHETASE (ASPRS) (E.C. 6.1.1.12) FROM YEAST

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTYL-TRNA SYNTHETASE

Saccharomyces cerevisiae

UniProt P04802

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 70–556 Fragment：ENGINEERED ASPRS MONOMER LACKING THE 70 N-TERMINAL AMINO ACID RESIDUES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；278 K；15 MG/ML PROTEIN, 1.9 M AMMONIUM SULFATE, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K Resolution 2.30 Å R-free 0.242

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 1EOV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ASY CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF YEAST ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH TRNA ASP Deposited 1995-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 67–556（490 aa）
Chain B 67–556（490 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1ASZ THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION Deposited 1995-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 67–556（490 aa）
Chain B 67–556（490 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYDC_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–487； UniProt 70–556

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 1eov

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1eov
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1eov
Deposition date deposition_date2000-03-24
Structure title titleFREE ASPARTYL-TRNA SYNTHETASE (ASPRS) (E.C. 6.1.1.12) FROM YEAST
Keywords keywordsaminoacyl tRNA synthetase, tRNA ligase, apo-enzyme, OB-fold, LIGASE; LIGASE
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_guinier28.50 Å
Radius of gyration Rg (electron density) rg_electron27.84 Å
Forward intensity I(0) i049618700.00
Molecular weight molecular_weight55580.0 kDa
Excluded volume excluded_volume69974 ų
Envelope volume envelope_volume91119 ų
Hydration-shell volume shell_volume28418 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg34.05 Å
Envelope Rg envelope_rg27.87 Å
Shape Rg shape_rg27.81 Å
Total Rg total_rg28.60 Å
Total atoms total_atoms3921
Residues n_residues487
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 dmax93.8 Å
Rg (real space) rg_real28.67 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real4.9620e+07
I(0) uncertainty (real space) i0_real_error7.5180e+05
Rg (reciprocal space) rg_reciprocal28.62 Å
I(0) (reciprocal space) i0_reciprocal49620000.0000
Solution quality estimate total_estimate0.7036
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.444
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8869000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.902; Smooth: 0.937
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1eova1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.1 — Anticodon-binding domain
Domain ID domain_idd1eova2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id1eovA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1eovA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
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8. Citations (5)

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9. Files and Curves (10)