SAXSdb — 7tf6

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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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–446 Chain B； UniProt 1–446 Chain C； UniProt 1–446 Chain F； UniProt 1–446 Chain G； UniProt 1–446 Chain H； UniProt 1–446 Chain L； UniProt 1–446 Chain N； UniProt 1–446 Chain O； UniProt 1–446 Chain R； UniProt 1–446 Chain S； UniProt 1–446 Chain T； UniProt 1–446	Not recorded	Peptide from Glutamine synthetase repressor × 12 （Q53687） 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

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 7TF6	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 oligomeric state 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
7TF7 S. aureus GS(12) - apo Deposited 2022-01-06	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 F； PDBConstruct 4–449； UniProt 1–446 Author chain G； PDBConstruct 4–449； UniProt 1–446 Author chain H； PDBConstruct 4–449； UniProt 1–446 Author chain L； PDBConstruct 4–449； UniProt 1–446 Author chain N； PDBConstruct 4–449； UniProt 1–446 Author chain O； PDBConstruct 4–449； UniProt 1–446 Author chain R； PDBConstruct 4–449； UniProt 1–446 Author chain S； PDBConstruct 4–449； UniProt 1–446 Author chain T； PDBConstruct 4–449； UniProt 1–446

Peptide from Glutamine synthetase repressor

OrganismNot specified

UniProt Q53687

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain D； UniProt 111–121 Chain E； UniProt 111–121 Chain I； UniProt 111–121 Chain J； UniProt 111–121 Chain K； UniProt 111–121 Chain M； UniProt 111–121 Chain P； UniProt 111–121 Chain Q； UniProt 111–121 Chain U； UniProt 111–121 Chain V； UniProt 111–121 Chain W； UniProt 111–121 Chain X； UniProt 111–121	Fragment：Residues 111-121	Glutamine synthetase × 12 （E3VXC2） 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

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 7TF6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TEA Crystal structure of S. aureus GlnR-DNA complex Deposited 2022-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain B 1–83（83 aa） Chain E 1–83（83 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；275 K；50 mM sodium cacodylate pH 6.5, 13% PEG 8000, 0.15 M calcium acetate, 20% glycerol	Resolution 2.35 Å R-free 0.264
7TEA Crystal structure of S. aureus GlnR-DNA complex Deposited 2022-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–83（83 aa） Chain C 1–83（83 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；275 K；50 mM sodium cacodylate pH 6.5, 13% PEG 8000, 0.15 M calcium acetate, 20% glycerol	Resolution 2.35 Å R-free 0.264

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

View Construct and Data Evidence

UniProt name	Q53687_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–11； UniProt 111–121 Author chain E； PDBConstruct 1–11； UniProt 111–121 Author chain I； PDBConstruct 1–11； UniProt 111–121 Author chain J； PDBConstruct 1–11； UniProt 111–121 Author chain K； PDBConstruct 1–11； UniProt 111–121 Author chain M； PDBConstruct 1–11； UniProt 111–121 Author chain P； PDBConstruct 1–11； UniProt 111–121 Author chain Q； PDBConstruct 1–11； UniProt 111–121 Author chain U； PDBConstruct 1–11； UniProt 111–121 Author chain V； PDBConstruct 1–11； UniProt 111–121 Author chain W； PDBConstruct 1–11； UniProt 111–121 Author chain X； PDBConstruct 1–11； UniProt 111–121

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	7tf6
Deposition date deposition_date	2022-01-06
Structure title title	S. aureus GS(12)-Q-GlnR peptide
Keywords keywords	glutamine synthetase repressor dodecamer, BIOSYNTHETIC PROTEIN, LIGASE; BIOSYNTHETIC PROTEIN, LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	54.66 Å
Radius of gyration Rg (electron density) rg_electron	54.02 Å
Forward intensity I(0) i0	5201270000.00
Molecular weight molecular_weight	612280.0 kDa
Excluded volume excluded_volume	766480 Å³
Envelope volume envelope_volume	1032400 Å³
Hydration-shell volume shell_volume	147290 Å³
Envelope diameter envelope_diameter	161.4 Å
Shell Rg shell_rg	67.08 Å
Envelope Rg envelope_rg	52.13 Å
Shape Rg shape_rg	53.99 Å
Total Rg total_rg	54.37 Å
Total atoms total_atoms	43272
Residues n_residues	5388
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	162.0 Å
Rg (real space) rg_real	54.23 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	5.2010e+09
I(0) uncertainty (real space) i0_real_error	8.7930e+07
Rg (reciprocal space) rg_reciprocal	55.01 Å
I(0) (reciprocal space) i0_reciprocal	5207000000.0000
Solution quality estimate total_estimate	0.8193
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	78.2 Å
Skewness Skewness skewness	-0.095
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	757100000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.000

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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	Glutamine synthetase
Molecular weight formula_weight	51196.8 kDa
EC 编号 ec_number	6.3.1.2
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,F,G,H,L,N,O,R,S,T
Atom count atom_count	43272

GSHMPKRTFTKEDIRKFAEEENVRYLRLQFTDILGTIKNVEVPVSQLEKVLDNEMMFDGSSIEGFVRIEESDMYLHPDLDTWVIFPWTAGQGKVARLICDVYKTDGTPFEGDPRANLKRVLKEMEDLGFTDFNLGPEPEFFLFKLDEKGEPTLELNDDGGYFDLAPTDLGENCRRDIVLELEDMGFDIEASHHEVAPGQHEIDFKYADAVTACDNIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMHFNVSLFKGKENAFFDPNTEMGLTETAYQFTAGVLKNARGFTAVCNPLVNSYKRLVPGYEAPCYIAWSGKNRSPLIRVPSSRGLSTRIEVRSVDPAANPYMALAAILEAGLDGIKNKLKVPEPVNQNIYEMNREEREAVGIQDLPSTLYTALKAMRENEVIKKALGNHIYNQFINSKSIEWDYYRTQVSEWERDQYMKQY

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 polymer

Description description	Peptide from Glutamine synthetase repressor
Molecular weight formula_weight	1289.5 kDa
Source method src_method	syn
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,I,J,K,M,P,Q,U,V,W,X

PINRGDLSRFI

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 non-polymer

Description description	GLUTAMINE
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	12

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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	—

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

Resolution resolution	2.15 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	222918

fit	/app/data/saxs_computation/tf/7tf6/7tf6.fit
pddf	/app/data/pr_computation/tf/7tf6/7tf6.pr.out
profile	/app/data/saxs_computation/tf/7tf6/7tf6.dat

S. aureus GS(12)-Q-GlnR peptide

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

Peptide from Glutamine synthetase repressor

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)