SAXSdb — 1c0a

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTYL TRNA SYNTHETASE

Escherichia coli

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–585	Not recorded	ASPARTYL TRNA × 1 SO4 SULFATE ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 AMO ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；AMMONIUM SULFATE, GLYCEROL, BIS-TRIS-PROPANE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.249

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 1C0A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EQR CRYSTAL STRUCTURE OF FREE ASPARTYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI Deposited 2000-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–590（590 aa） Chain B 1–590（590 aa） Chain C 1–590（590 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ammonium sulphate, Bis Tris propane, isopropanol, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
1IL2 Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex Deposited 2001-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–590（590 aa）	Not recorded	SO4 SULFATE ION × 1 AMO ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.60 Å R-free 0.257
1IL2 Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex Deposited 2001-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–590（590 aa）	Not recorded	SO4 SULFATE ION × 1 AMO ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.60 Å R-free 0.257

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

View Construct and Data Evidence

UniProt name	SYD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–585； UniProt 1–585

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_id	1c0a
Deposition date deposition_date	1999-07-15
Structure title title	CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX
Keywords keywords	PROTEIN-RNA COMPLEX, LIGASE-RNA COMPLEX; LIGASE/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.73 Å
Radius of gyration Rg (electron density) rg_electron	31.30 Å
Forward intensity I(0) i0	191405000.00
Molecular weight molecular_weight	91385.0 kDa
Excluded volume excluded_volume	106140 Å³
Envelope volume envelope_volume	142550 Å³
Hydration-shell volume shell_volume	38363 Å³
Envelope diameter envelope_diameter	100.3 Å
Shell Rg shell_rg	38.12 Å
Envelope Rg envelope_rg	30.81 Å
Shape Rg shape_rg	31.28 Å
Total Rg total_rg	31.82 Å
Total atoms total_atoms	6306
Residues n_residues	653
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.9 Å
Rg (real space) rg_real	31.62 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.9140e+08
I(0) uncertainty (real space) i0_real_error	3.1160e+06
Rg (reciprocal space) rg_reciprocal	31.67 Å
I(0) (reciprocal space) i0_reciprocal	191400000.0000
Solution quality estimate total_estimate	0.9104
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.129
Kurtosis Kurtosis kurtosis	-0.660
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18080000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.946

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ASPARTYL TRNA
Molecular weight formula_weight	24995.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	6820

GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAGUCCCGUCCGUUCCGCCA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ASPARTYL TRNA SYNTHETASE
Molecular weight formula_weight	65438.7 kDa
EC 编号 ec_number	6.1.1.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLASSLTIINRADVLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKFYALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREVMEALVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLRNPMELTDVADLLKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLAYIKVNERAKGLEGINSPVAKFLNAEIIEDILDRTAAQDGDMIFFGADNKKIVADAMGALRLKVGKDLGLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTAAELKAAPENAVANAYDMVINGYEVGGGSVRIHNGDMQQTVFGILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQVVK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	462.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	514

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c0aa1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.1 — Anticodon-binding domain

Domain ID domain_id	d1c0aa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.4 — GAD domain-like
Family Family family	d.74.4.1 — GAD domain

Domain ID domain_id	d1c0aa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	1c0aA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1c0aA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	1c0aA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	30 — GAD-like domain

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8. Citations (1)

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Unit-cell length a length_a	101.200 Å
Unit-cell length b length_b	101.200 Å
Unit-cell length c length_c	231.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2490

fit	/app/data/saxs_computation/c0/1c0a/1c0a.fit
pddf	/app/data/pr_computation/c0/1c0a/1c0a.pr.out
profile	/app/data/saxs_computation/c0/1c0a/1c0a.dat

CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX

1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTYL TRNA SYNTHETASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)