SAXSdb — 7tea

▼

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

Glutamine synthetase repressor

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 1–83 Chain E； UniProt 1–83	Not recorded	;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPAPAPTPCPTPGPAPCPAPCPG)-3') ; × 1 ;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPTPAPTPCPTPGPAPCPAPCPG)-3') ; × 1 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
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–83 Chain C； UniProt 1–83	Not recorded	;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPAPAPTPCPTPGPAPCPAPCPG)-3') ; × 1 ;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPTPAPTPCPTPGPAPCPAPCPG)-3') ; × 1 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

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 7TEA	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 D 111–121（11 aa） Fragment：Residues 111-121 Chain E 111–121（11 aa） Fragment：Residues 111-121 Chain I 111–121（11 aa） Fragment：Residues 111-121 Chain J 111–121（11 aa） Fragment：Residues 111-121 Chain K 111–121（11 aa） Fragment：Residues 111-121 Chain M 111–121（11 aa） Fragment：Residues 111-121 Chain P 111–121（11 aa） Fragment：Residues 111-121 Chain Q 111–121（11 aa） Fragment：Residues 111-121 Chain U 111–121（11 aa） Fragment：Residues 111-121 Chain V 111–121（11 aa） Fragment：Residues 111-121 Chain W 111–121（11 aa） Fragment：Residues 111-121 Chain X 111–121（11 aa） Fragment：Residues 111-121	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

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

View Construct and Data Evidence

UniProt name	Q53687_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–86； UniProt 1–83 Author chain B； PDBConstruct 4–86； UniProt 1–83 Author chain C； PDBConstruct 4–86； UniProt 1–83 Author chain E； PDBConstruct 4–86； UniProt 1–83

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	7tea
Deposition date deposition_date	2022-01-04
Structure title title	Crystal structure of S. aureus GlnR-DNA complex
Keywords keywords	;GlnR, winged-HTH, S. aureus, femC, glutamine synthetase, transcription repressor, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.36 Å
Radius of gyration Rg (electron density) rg_electron	37.21 Å
Forward intensity I(0) i0	93397200.00
Molecular weight molecular_weight	62330.0 kDa
Excluded volume excluded_volume	71406 Å³
Envelope volume envelope_volume	110690 Å³
Hydration-shell volume shell_volume	25583 Å³
Envelope diameter envelope_diameter	125.2 Å
Shell Rg shell_rg	41.86 Å
Envelope Rg envelope_rg	36.07 Å
Shape Rg shape_rg	37.20 Å
Total Rg total_rg	37.50 Å
Total atoms total_atoms	4277
Residues n_residues	392
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	125.2 Å
Rg (real space) rg_real	37.65 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	9.3400e+07
I(0) uncertainty (real space) i0_real_error	1.5990e+06
Rg (reciprocal space) rg_reciprocal	37.48 Å
I(0) (reciprocal space) i0_reciprocal	93380000.0000
Solution quality estimate total_estimate	0.8109
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.306
Kurtosis Kurtosis kurtosis	-0.755
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3595000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.625; Smooth: 0.700

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Glutamine synthetase repressor
Molecular weight formula_weight	10141.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,A,C
Atom count atom_count	4368

GSHMISNDAIRRNMAVFSMSVVSKLTDLTPRQIRYYETHELIKPERTEGQKRLFSLNDLERLLEIKSLLEKGFNIKEIKQIIYDSQ

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	;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPAPAPTPCPTPGPAPCPAPCP*G)-3') ;
Molecular weight formula_weight	6447.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,D

CGTGTCAGATAATCTGACACG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPGPTPGPTPCPAPGPAPTPTPAPTPCPTPGPAPCPAPCP*G)-3') ;
Molecular weight formula_weight	6438.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

CGTGTCAGATTATCTGACACG

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

▶

8. Citations (1)

▶

Unit-cell length a length_a	66.502 Å
Unit-cell length b length_b	99.265 Å
Unit-cell length c length_c	238.922 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	32

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	49.630 Å
R factor r_factor	0.2159
R_work r_work	0.2126
R_free r_free	0.2635

fit	/app/data/saxs_computation/te/7tea/7tea.fit
pddf	/app/data/pr_computation/te/7tea/7tea.pr.out
profile	/app/data/saxs_computation/te/7tea/7tea.dat

Crystal structure of S. aureus GlnR-DNA complex

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

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)