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1b8a

ASPARTYL-TRNA SYNTHETASE

Method: X-RAY DIFFRACTION Dmax: 101.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ASPARTYL-TRNA SYNTHETASE)

Thermococcus kodakarensis

UniProt Q52428

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 1–438 Chain B； UniProt 1–438 Not recorded MN MANGANESE (II) ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5 Resolution 1.90 Å R-free 0.202

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 1B8A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3NEL Aspartyl-tRNA synthetase complexed with aspartic acid Deposited 2010-06-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–438（438 aa）
Chain B 1–438（438 aa）
Not recorded ASP ASPARTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；peg and ethylen glycol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.95 Å R-free 0.236
3NEM Aspartyl-tRNA synthetase complexed with aspartyl adenylate Deposited 2010-06-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–438（438 aa）
Chain B 1–438（438 aa）
Not recorded AMO ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 297 K；peg and ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.89 Å R-free 0.213
3NEN Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis Deposited 2010-06-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–438（438 aa）
Chain B 1–438（438 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 297 K；peg and ethylen glycol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.40 Å R-free 0.265

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYD_PYRKO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–438； UniProt 1–438 Author chain B； PDBConstruct 1–438； UniProt 1–438

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 1b8a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b8a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b8a
Deposition date deposition_date1999-01-27
Structure title titleASPARTYL-TRNA SYNTHETASE
Keywords keywordsSYNTHETASE, TRNA LIGASE, 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_guinier29.85 Å
Radius of gyration Rg (electron density) rg_electron29.37 Å
Forward intensity I(0) i0161529000.00
Molecular weight molecular_weight103130.0 kDa
Excluded volume excluded_volume129720 ų
Envelope volume envelope_volume153640 ų
Hydration-shell volume shell_volume42571 ų
Envelope diameter envelope_diameter109.0 Å
Shell Rg shell_rg37.53 Å
Envelope Rg envelope_rg29.86 Å
Shape Rg shape_rg29.36 Å
Total Rg total_rg30.10 Å
Total atoms total_atoms7256
Residues n_residues876
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 dmax101.5 Å
Rg (real space) rg_real29.78 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real1.6150e+08
I(0) uncertainty (real space) i0_real_error2.4420e+06
Rg (reciprocal space) rg_reciprocal29.81 Å
I(0) (reciprocal space) i0_reciprocal161500000.0000
Solution quality estimate total_estimate0.6580
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4 Å
Skewness Skewness skewness0.304
Kurtosis Kurtosis kurtosis-0.297
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45050000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 0.999; Smooth: 0.981
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1b8aa1
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_idd1b8aa2
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
Domain ID domain_idd1b8ab1
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_idd1b8ab2
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 (4 domains)

Domain ID domain_id1b8aA01
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_id1b8aA02
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
Domain ID domain_id1b8aB01
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_id1b8aB02
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 (1)

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9. Files and Curves (10)