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3fhj

Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tryptophanyl-tRNA synthetase

Bacillus stearothermophilus

UniProt P00953

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 TRYPTOPHAN × 2 PHOSPHATE ION × 2 ADENOSINE MONOPHOSPHATE × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 TRYPTOPHAN × 2 PHOSPHATE ION × 2 ADENOSINE MONOPHOSPHATE × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 TRYPTOPHAN × 2 PHOSPHATE ION × 2 ADENOSINE MONOPHOSPHATE × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1d2r 1d2r 1d2r 1i6k 1i6l 1i6m 1m83 1mau 1maw 1maw 1maw 1mb2

33 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name SYW_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–326； UniProt 1–328 Author chain B； PDBConstruct 1–326； UniProt 1–328 Author chain C； PDBConstruct 1–326； UniProt 1–328 Author chain D； PDBConstruct 1–326； UniProt 1–328 Author chain E； PDBConstruct 1–326； UniProt 1–328 Author chain F； PDBConstruct 1–326； UniProt 1–328

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fhj
Deposition date deposition_date2008-12-09
Structure title titleIndependent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations
Keywords keywords;ligand-dependent domain rearrangement, mechanistic pathway, molecular simulations, Aminoacyl-tRNA synthetase, ATP-binding, Cytoplasm, Ligase, Nucleotide-binding, Protein biosynthesis, TRANSLATION ;; TRANSLATION
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3fhj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fhj__assembly_2__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3fhj__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）29.40 Å
Rg (electron density)29.51 Å
Total Rg29.94 Å
Atom count4592
Residues565
Excluded volume82035 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3fhj__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3fhj__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3fhj__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3fhja_
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
Domain ID domain_idd3fhjb_
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
Domain ID domain_idd3fhjc_
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
Domain ID domain_idd3fhjd_
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
Domain ID domain_idd3fhje_
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
Domain ID domain_idd3fhjf_
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 (12 domains)

Domain ID domain_id3fhjA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
Domain ID domain_id3fhjB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
Domain ID domain_id3fhjC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
Domain ID domain_id3fhjD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
Domain ID domain_id3fhjE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
Domain ID domain_id3fhjF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3fhjF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
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7. Citations (1)