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1a8h

METHIONYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS

Method: X-RAY DIFFRACTION Dmax: 92.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

METHIONYL-TRNA SYNTHETASE

OrganismNot specified

UniProt P23395

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–500 Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5 Resolution 2.00 Å R-free 0.283

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 1A8H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WOY Crystal structure of methionyl tRNA synthetase Y225F mutant from Thermus thermophilus Deposited 2004-08-27 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa） Fragment：residues 1-500
Mutation：Y225F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2-propanol, sodium citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.226
2D54 Crystal Structure of Methionyl tRNA Synthetase Y225A Mutant from Thermus Thermophilus Deposited 2005-10-28 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–502（502 aa） Fragment：MetRS
Mutation：Y225A ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG6000, 0.1M Hepes-Na, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.254
2D5B Crystal Structure of Thermus Thermophilus Methionyl tRNA synthetase Y225F Mutant obtained in the presence of PEG6000 Deposited 2005-10-31 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa） Fragment：MetRS
Mutation：Y225F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG6000, Hepes-Na(0.1M), DTT(1mM), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.242
3VU8 Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue Deposited 2012-06-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–502（502 aa） Fragment：UNP residues 1-502
Not recorded ZN ZINC ION × 1 MDS N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG6000, DTT, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.300

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYM_THET8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–500； UniProt 1–500

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 1a8h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a8h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a8h
Deposition date deposition_date1998-03-26
Structure title titleMETHIONYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Keywords keywordsAMINOACYL-TRNA SYNTHETASE, ROSSMANN FOLD, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics; AMINOACYL-TRNA SYNTHETASE
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_guinier27.28 Å
Radius of gyration Rg (electron density) rg_electron26.56 Å
Forward intensity I(0) i052176000.00
Molecular weight molecular_weight57998.0 kDa
Excluded volume excluded_volume73264 ų
Envelope volume envelope_volume87317 ų
Hydration-shell volume shell_volume28694 ų
Envelope diameter envelope_diameter97.9 Å
Shell Rg shell_rg32.63 Å
Envelope Rg envelope_rg26.73 Å
Shape Rg shape_rg26.54 Å
Total Rg total_rg27.29 Å
Total atoms total_atoms4102
Residues n_residues500
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 dmax92.9 Å
Rg (real space) rg_real27.45 Å
Rg uncertainty (real space) rg_real_error0.97 Å
I(0) (real space) i0_real5.2180e+07
I(0) uncertainty (real space) i0_real_error9.4680e+05
Rg (reciprocal space) rg_reciprocal27.40 Å
I(0) (reciprocal space) i0_reciprocal52170000.0000
Solution quality estimate total_estimate0.8094
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4 Å
Skewness Skewness skewness0.552
Kurtosis Kurtosis kurtosis-0.077
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8254000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.279
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1a8ha1
Class classa — All alpha proteins
Fold Fold folda.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamilya.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family Family familya.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Domain ID domain_idd1a8ha2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamilyc.26.1 — Nucleotidylyl transferase
Family Family familyc.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id1a8hA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id1a8hA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology220 — Methionyl-trna Synthetase; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1a8hA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology730 — Isoleucyl-tRNA Synthetase; Domain 1
Homologous superfamily homologous superfamily10 — Isoleucyl-tRNA Synthetase; Domain 1
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8. Citations (1)

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9. Files and Curves (10)