SAXSdb — 7tdv

▼

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

Glutamine synthetase

Staphylococcus aureus

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: dodecameric（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 H； UniProt 1–446	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

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 7TDV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TF6 S. aureus GS(12)-Q-GlnR peptide Deposited 2022-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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
9Y4A His-tagged Glutamine Synthetase on a Ni-NTA lipid monolayer grid Deposited 2025-09-02	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: 12-meric	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 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 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 4–449； UniProt 1–446 Author chain B； PDBConstruct 4–449； UniProt 1–446 Author chain C； PDBConstruct 4–449； UniProt 1–446 Author chain D； PDBConstruct 4–449； UniProt 1–446 Author chain E； PDBConstruct 4–449； UniProt 1–446 Author chain H； PDBConstruct 4–449； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7tdv
Deposition date deposition_date	2022-01-03
Structure title title	Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex
Keywords keywords	Glutamine synthetase, glutamate-ammonium ligase, GlnR, S. aureus, femC, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	49.65 Å
Radius of gyration Rg (electron density) rg_electron	49.11 Å
Forward intensity I(0) i0	1360980000.00
Molecular weight molecular_weight	305690.0 kDa
Excluded volume excluded_volume	380860 Å³
Envelope volume envelope_volume	535000 Å³
Hydration-shell volume shell_volume	86941 Å³
Envelope diameter envelope_diameter	151.2 Å
Shell Rg shell_rg	57.84 Å
Envelope Rg envelope_rg	47.13 Å
Shape Rg shape_rg	49.09 Å
Total Rg total_rg	49.43 Å
Total atoms total_atoms	21626
Residues n_residues	2654
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

▼

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

Maximum dimension Dmax dmax	151.6 Å
Rg (real space) rg_real	49.35 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	1.3610e+09
I(0) uncertainty (real space) i0_real_error	2.4530e+07
Rg (reciprocal space) rg_reciprocal	49.65 Å
I(0) (reciprocal space) i0_reciprocal	1361000000.0000
Solution quality estimate total_estimate	0.8953
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	75.8 Å
Skewness Skewness skewness	0.013
Kurtosis Kurtosis kurtosis	-0.807
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	261400000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.792

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Glutamine synthetase
Molecular weight formula_weight	51224.9 kDa
EC 编号 ec_number	6.3.1.2
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,E,B,H
Atom count atom_count	21932

GSHMPKRTFTKEDIRKFVEEENVRYLRLQFTDILGTIKNVEVPVSQLEKVLDNEMMFDGSSIEGFVRIEESDMYLHPDLDTWVIFPWTAGQGKVARLICDVYKTDGTPFEGDPRANLKRVLKEMEDLGFTDFNLGPEPEFFLFKLDEKGEPTLELNDDGGYFDLAPTDLGENCRRDIVLELEDMGFDIEASHHEVAPGQHEIDFKYADAVTACDNIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMHFNVSLFKGKENAFFDPNTEMGLTETAYQFTAGVLKNARGFTAVCNPLVNSYKRLVPGYEAPCYIAWSGKNRSPLIRVPSSRGLSTRIEVRSVDPAANPYMALAAILEAGLDGIKNKLKVPEPVNQNIYEMNREEREAVGIQDLPSTLYTALKAMRENEVIKKALGNHIYNQFINSKSIEWDYYRTQVSEWERDQYMKQY

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	L-METHIONINE-S-SULFOXIMINE PHOSPHATE
Molecular weight formula_weight	260.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	306

▶

8. Citations (1)

▶

Unit-cell length a length_a	154.615 Å
Unit-cell length b length_b	154.615 Å
Unit-cell length c length_c	299.295 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	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.920 Å
Low-resolution limit resolution_low	48.890 Å
R factor r_factor	0.1997
R_work r_work	0.1984
R_free r_free	0.2561

fit	/app/data/saxs_computation/td/7tdv/7tdv.fit
pddf	/app/data/pr_computation/td/7tdv/7tdv.pr.out
profile	/app/data/saxs_computation/td/7tdv/7tdv.dat

Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex

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

Glutamine 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