SAXSdb — 1ati

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

GLYCYL-TRNA SYNTHETASE

OrganismNot specified

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–505 Chain B； UniProt 1–505	Not recorded	GLYCYL-tRNA SYNTHETASE × 1 GLYCYL-tRNA SYNTHETASE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.75 Å R-free 0.290

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 1ATI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B76 GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP Deposited 1999-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–96（95 aa） Chain A 160–506（347 aa） Chain B 2–96（95 aa） Chain B 160–506（347 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；297 K；pH 8.0, temperature 297K	Resolution 3.40 Å R-free 0.318
1GGM GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE Deposited 1999-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–96（95 aa） Chain A 160–506（347 aa） Chain B 2–96（95 aa） Chain B 160–506（347 aa）	Not recorded	GAP GLYCYL-ADENOSINE-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；297 K；pH 8.0, temperature 297K	Resolution 3.40 Å R-free 0.334

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

View Construct and Data Evidence

UniProt name	SYG_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–505； UniProt 1–505 Author chain B； PDBConstruct 1–505； UniProt 1–505

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	1ati
Deposition date deposition_date	1996-04-23
Structure title title	CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Keywords keywords	PROTEIN BIOSYNTHESIS, LIGASE, SYNTHETASE, AMINOACYL-TRNA SYNTHETASE; PROTEIN BIOSYNTHESIS
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	30.39 Å
Radius of gyration Rg (electron density) rg_electron	29.06 Å
Forward intensity I(0) i0	174110000.00
Molecular weight molecular_weight	104360.0 kDa
Excluded volume excluded_volume	130400 Å³
Envelope volume envelope_volume	163010 Å³
Hydration-shell volume shell_volume	44969 Å³
Envelope diameter envelope_diameter	104.4 Å
Shell Rg shell_rg	37.76 Å
Envelope Rg envelope_rg	29.50 Å
Shape Rg shape_rg	29.07 Å
Total Rg total_rg	29.82 Å
Total atoms total_atoms	7384
Residues n_residues	926
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	95.7 Å
Rg (real space) rg_real	30.23 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.7410e+08
I(0) uncertainty (real space) i0_real_error	2.1550e+06
Rg (reciprocal space) rg_reciprocal	30.30 Å
I(0) (reciprocal space) i0_reciprocal	174100000.0000
Solution quality estimate total_estimate	0.8900
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.6 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42470000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.918

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	GLYCYL-TRNA SYNTHETASE
Molecular weight formula_weight	58164.0 kDa
EC 编号 ec_number	6.1.1.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7407

AASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWWRRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDNRITKKRYRLDHLLKEQPEEVLKRLYRAMEVEEENLHALVQAMMQAPERAGGAMTAAGVLDPASGEPGDWTPPRYFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKWWQEMGLSRENLVPYQQPPESSAHYAKATVDILYRFPHGSLELEGIAQRTDFDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW

Entity 2 Entity 2 polymer

Description description	GLYCYL-tRNA SYNTHETASE
Molecular weight formula_weight	3166.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 3 Entity 3 polymer

Description description	GLYCYL-tRNA SYNTHETASE
Molecular weight formula_weight	1379.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XXXXXXXXXXXXXXXX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1atia1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1atia2
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

Domain ID domain_id	d1atib1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1atib2
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 (4 domains)

Domain ID domain_id	1atiA01
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	1atiA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1atiB01
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	1atiB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

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8. Citations (2)

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Unit-cell length a length_a	126.900 Å
Unit-cell length b length_b	255.300 Å
Unit-cell length c length_c	105.000 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2900

fit	/app/data/saxs_computation/at/1ati/1ati.fit
pddf	/app/data/pr_computation/at/1ati/1ati.pr.out
profile	/app/data/saxs_computation/at/1ati/1ati.dat

CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS

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

GLYCYL-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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)