SAXSdb — 1d2d

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

TRNA SYNTHETASE

Cricetulus griseus

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 1–49	Fragment：RESIDUES 1-59	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Pressure 1 NMR sample composition：1.5 MM EPRS REPEAT U-15N; 20 MM POTASSIUM PHOSPHATE PH 7.0, 5 MM DITHIOTHREITOL, 0.5 MM NAN3;	Resolution not provided

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 1D2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1R1B EPRS SECOND REPEATED ELEMENT, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-12-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–49（49 aa） Fragment：RESIDUES 1 - 59	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Pressure 1	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYEP_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–51； UniProt 1–49

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	1d2d
Deposition date deposition_date	1999-09-23
Structure title title	Hamster EprS second repeated element. NMR, 5 structures
Keywords keywords	TRNA SYNTHETASE (LIGASE), PROTEIN TRANSCRIPTION, LIGASE; LIGASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.50 Å
Radius of gyration Rg (electron density) rg_electron	11.47 Å
Forward intensity I(0) i0	14089600.00
Molecular weight molecular_weight	31392.0 kDa
Excluded volume excluded_volume	39951 Å³
Envelope volume envelope_volume	11423 Å³
Hydration-shell volume shell_volume	8357 Å³
Envelope diameter envelope_diameter	46.0 Å
Shell Rg shell_rg	17.33 Å
Envelope Rg envelope_rg	12.86 Å
Shape Rg shape_rg	11.39 Å
Total Rg total_rg	12.23 Å
Total atoms total_atoms	4525
Residues n_residues	280
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	41.4 Å
Rg (real space) rg_real	11.55 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.4090e+07
I(0) uncertainty (real space) i0_real_error	1.5430e+05
Rg (reciprocal space) rg_reciprocal	11.55 Å
I(0) (reciprocal space) i0_reciprocal	14090000.0000
Solution quality estimate total_estimate	0.7359
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	12.6 Å
Skewness Skewness skewness	0.432
Kurtosis Kurtosis kurtosis	-0.118
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	65970.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2da1
Class class	a — All alpha proteins
Fold Fold fold	a.16 — S15/NS1 RNA-binding domain
Superfamily Superfamily superfamily	a.16.1 — S15/NS1 RNA-binding domain
Family Family family	a.16.1.3 — a tRNA synthase domain

Domain ID domain_id	d1d2da2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1d2dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	10 — S15/NS1, RNA-binding

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	TRNA SYNTHETASE
Molecular weight formula_weight	6721.8 kDa
EC 编号 ec_number	6.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4525

来源生物 organism	Cricetulus griseus
通用名 common_name	Chinese hamster
NCBI Class编号 ncbi_taxonomy_id	10029
宿主生物 host_organism	Escherichia coli

Hamster EprS second repeated element. NMR, 5 structures

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

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/d2/1d2d/1d2d.fit
pddf	/app/data/pr_computation/d2/1d2d/1d2d.pr.out
profile	/app/data/saxs_computation/d2/1d2d/1d2d.dat