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9y4a

His-tagged Glutamine Synthetase on a Ni-NTA lipid monolayer grid

Method: ELECTRON MICROSCOPY Dmax: 161.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamine synthetase

Staphylococcus aureus

UniProt E3VXC2

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 × 12 PDB declaration: 12-meric（12） Consistent with protein copy count Chain A； UniProt 1–446 Chain B； UniProt 1–446 Chain C； UniProt 1–446 Chain D； UniProt 1–446 Chain E； UniProt 1–446 Chain F； UniProt 1–446 Chain G； UniProt 1–446 Chain H； UniProt 1–446 Chain I； UniProt 1–446 Chain J； UniProt 1–446 Chain K； UniProt 1–446 Chain L； UniProt 1–446 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.10 Å

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 9Y4A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7TDV Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex Deposited 2022-01-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 1–446（446 aa）
Chain B 1–446（446 aa）
Chain C 1–446（446 aa）
Chain D 1–446（446 aa）
Chain E 1–446（446 aa）
Chain H 1–446（446 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 12 P3S L-METHIONINE-S-SULFOXIMINE PHOSPHATE × 12 MG MAGNESIUM ION × 42 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；28% Peg 400, 0.2 M calcium chloride, 0.1 M HEPES 7.5
Resolution 2.92 Å R-free 0.256
7TF6 S. aureus GS(12)-Q-GlnR peptide Deposited 2022-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–446（446 aa）
Chain B 1–446（446 aa）
Chain C 1–446（446 aa）
Chain F 1–446（446 aa）
Chain G 1–446（446 aa）
Chain H 1–446（446 aa）
Chain L 1–446（446 aa）
Chain N 1–446（446 aa）
Chain O 1–446（446 aa）
Chain R 1–446（446 aa）
Chain S 1–446（446 aa）
Chain T 1–446（446 aa）
Not recorded MG MAGNESIUM ION × 24 GLN GLUTAMINE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.15 Å
7TF7 S. aureus GS(12) - apo Deposited 2022-01-06 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 1–446（446 aa）
Chain B 1–446（446 aa）
Chain C 1–446（446 aa）
Chain D 1–446（446 aa）
Chain E 1–446（446 aa）
Chain F 1–446（446 aa）
Chain G 1–446（446 aa）
Chain H 1–446（446 aa）
Chain I 1–446（446 aa）
Chain J 1–446（446 aa）
Chain K 1–446（446 aa）
Chain L 1–446（446 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.13 Å

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

View Construct and Data Evidence
UniProt name E3VXC2_STAAU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–466； UniProt 1–446 Author chain B； PDBConstruct 21–466； UniProt 1–446 Author chain C； PDBConstruct 21–466； UniProt 1–446 Author chain D； PDBConstruct 21–466； UniProt 1–446 Author chain E； PDBConstruct 21–466； UniProt 1–446 Author chain F； PDBConstruct 21–466； UniProt 1–446 Author chain G； PDBConstruct 21–466； UniProt 1–446 Author chain H； PDBConstruct 21–466； UniProt 1–446 Author chain I； PDBConstruct 21–466； UniProt 1–446 Author chain J； PDBConstruct 21–466； UniProt 1–446 Author chain K； PDBConstruct 21–466； UniProt 1–446 Author chain L； PDBConstruct 21–466； UniProt 1–446

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 9y4a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y4a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y4a
Deposition date deposition_date2025-09-02
Structure title titleHis-tagged Glutamine Synthetase on a Ni-NTA lipid monolayer grid
Keywords keywordsEnzyme, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.69 Å
Radius of gyration Rg (electron density) rg_electron55.03 Å
Forward intensity I(0) i04367250000.00
Molecular weight molecular_weight565560.0 kDa
Excluded volume excluded_volume709750 ų
Envelope volume envelope_volume981670 ų
Hydration-shell volume shell_volume138090 ų
Envelope diameter envelope_diameter162.5 Å
Shell Rg shell_rg67.58 Å
Envelope Rg envelope_rg53.05 Å
Shape Rg shape_rg55.00 Å
Total Rg total_rg55.38 Å
Total atoms total_atoms39876
Residues n_residues4968
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 dmax161.4 Å
Rg (real space) rg_real55.24 Å
Rg uncertainty (real space) rg_real_error1.15 Å
I(0) (real space) i0_real4.3670e+09
I(0) uncertainty (real space) i0_real_error8.5240e+07
Rg (reciprocal space) rg_reciprocal56.06 Å
I(0) (reciprocal space) i0_reciprocal4372000000.0000
Solution quality estimate total_estimate0.8601
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary74.9 Å
Skewness Skewness skewness-0.090
Kurtosis Kurtosis kurtosis-0.558
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha287200000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.453
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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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8. Citations (1)

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9. Files and Curves (10)