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1ggm

GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE

Method: X-RAY DIFFRACTION Dmax: 92.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycine--tRNA ligase

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt P56206

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–96 Chain A； UniProt 160–506 Chain B； UniProt 2–96 Chain B； UniProt 160–506 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

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 1GGM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ATI CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS Deposited 1996-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–505（505 aa）
Chain B 1–505（505 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.75 Å R-free 0.290
1B76 GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP Deposited 1999-01-27 Different ligand/ion 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

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 1–95； UniProt 2–96 Author chain A； PDBConstruct 96–442； UniProt 160–506 Author chain B； PDBConstruct 1–95； UniProt 2–96 Author chain B； PDBConstruct 96–442； UniProt 160–506

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 1ggm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ggm
Deposition date deposition_date1999-01-27
Structure title titleGLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE
Keywords keywordsAMINOACYL-TRNA SYNTHASE, LIGASE(SYNTHETASE), LIGASE; LIGASE
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_guinier29.21 Å
Radius of gyration Rg (electron density) rg_electron28.05 Å
Forward intensity I(0) i0168743000.00
Molecular weight molecular_weight102740.0 kDa
Excluded volume excluded_volume128430 ų
Envelope volume envelope_volume151710 ų
Hydration-shell volume shell_volume43186 ų
Envelope diameter envelope_diameter96.6 Å
Shell Rg shell_rg36.90 Å
Envelope Rg envelope_rg28.40 Å
Shape Rg shape_rg28.04 Å
Total Rg total_rg28.86 Å
Total atoms total_atoms8957
Residues n_residues884
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 dmax92.8 Å
Rg (real space) rg_real29.05 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real1.6870e+08
I(0) uncertainty (real space) i0_real_error2.3780e+06
Rg (reciprocal space) rg_reciprocal29.12 Å
I(0) (reciprocal space) i0_reciprocal168800000.0000
Solution quality estimate total_estimate0.8909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.8 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha53030000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.976
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1ggma1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1ggma2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1ggmb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1ggmb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id1ggmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1ggmA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1ggmB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1ggmB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
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8. Citations (3)

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9. Files and Curves (10)