SAXSdb — 7smh

▼

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

Surface protein G

Staphylococcus aureus (strain NCTC 8325 / PS 47)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 144–423	Fragment：A domain (UNP residues 144-423)	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG3350, 0.2 M sodium malonate, pH 5.0	Resolution 1.65 Å R-free 0.226
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 144–423	Fragment：A domain (UNP residues 144-423)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG3350, 0.2 M sodium malonate, pH 5.0	Resolution 1.65 Å R-free 0.226
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 144–423	Fragment：A domain (UNP residues 144-423)	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG3350, 0.2 M sodium malonate, pH 5.0	Resolution 1.65 Å R-free 0.226
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 144–423	Fragment：A domain (UNP residues 144-423)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG3350, 0.2 M sodium malonate, pH 5.0	Resolution 1.65 Å R-free 0.226

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 7SMH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TIP Crystal structure of Staphylococcus aureus SasG E-G52 module Deposited 2011-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 502–629（128 aa） Fragment：UNP Residues 498-629	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；0.2M ammonium chloride, 20% PEG3350, pH 7.4, vapor diffusion sitting drop, temperature 293K	Resolution 1.70 Å R-free 0.239
3TIQ Crystal structure of Staphylococcus aureus SasG G51-E-G52 module Deposited 2011-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 419–629（211 aa） Fragment：UNP Residues 419-629	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M magnesium chloride, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, vapor diffusion sitting drop, temperature 293K	Resolution 1.87 Å R-free 0.266
3TIQ Crystal structure of Staphylococcus aureus SasG G51-E-G52 module Deposited 2011-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 419–629（211 aa） Fragment：UNP Residues 419-629	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M magnesium chloride, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, vapor diffusion sitting drop, temperature 293K	Resolution 1.87 Å R-free 0.266
4WVE Crystal structure of the Staphylococcus aureus SasG G52-E2-G53 module Deposited 2014-11-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 545–757（213 aa） Fragment：UNP residues 545-757	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 0.1 M HEPES, 30% PEG400, pH 7.5	Resolution 1.60 Å R-free 0.249
4WVE Crystal structure of the Staphylococcus aureus SasG G52-E2-G53 module Deposited 2014-11-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 545–757（213 aa） Fragment：UNP residues 545-757	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 0.1 M HEPES, 30% PEG400, pH 7.5	Resolution 1.60 Å R-free 0.249
5DBL Crystal structure of the Staphylococcus aureus SasG E1-G52 Y625W mutant Deposited 2015-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 502–629（128 aa） Fragment：UNP residues 498-629	Mutation：Y625W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；100 mM citrate pH 5, 20% PEG 6000	Resolution 1.60 Å R-free 0.207

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SASG_STAA8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–280； UniProt 144–423 Author chain B； PDBConstruct 1–280； UniProt 144–423 Author chain C； PDBConstruct 1–280； UniProt 144–423 Author chain D； PDBConstruct 1–280； UniProt 144–423

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	7smh
Deposition date deposition_date	2021-10-25
Structure title title	Structure of SASG A-domain (residues 163-419) from Staphylococcus aureus
Keywords keywords	CELL ADHESION, L-type lectin; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.94 Å
Radius of gyration Rg (electron density) rg_electron	34.14 Å
Forward intensity I(0) i0	207810000.00
Molecular weight molecular_weight	111940.0 kDa
Excluded volume excluded_volume	138250 Å³
Envelope volume envelope_volume	179070 Å³
Hydration-shell volume shell_volume	43237 Å³
Envelope diameter envelope_diameter	109.7 Å
Shell Rg shell_rg	41.58 Å
Envelope Rg envelope_rg	33.25 Å
Shape Rg shape_rg	34.11 Å
Total Rg total_rg	34.75 Å
Total atoms total_atoms	7894
Residues n_residues	1022
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	109.5 Å
Rg (real space) rg_real	34.81 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.0780e+08
I(0) uncertainty (real space) i0_real_error	3.6910e+06
Rg (reciprocal space) rg_reciprocal	34.90 Å
I(0) (reciprocal space) i0_reciprocal	207800000.0000
Solution quality estimate total_estimate	0.9031
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.1 Å
Skewness Skewness skewness	0.094
Kurtosis Kurtosis kurtosis	-0.678
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89150000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.932

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Surface protein G
Molecular weight formula_weight	30690.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8288

RSVDEGSFDITRDSKNVVESTPITIQGKEHFEGYGSVDIQKKPTDLGVSEVTRFNVGNESNGLIGALQLKNKIDFSKDFNFKVRVANNHQSNTTGADGWGFLFSKGNAEEYLTNGGILGDKGLVNSGGFKIDTGYIYTSSMDKTEKQAGQGYRGYGAFVKNDSSGNSQMVGENIDKSKTNFLNYADNSTNTSDGKFHGQRLNDVILTYVASTGKMRAEYAGKTWETSITDLGLSKNQAYNFLITSSQRWGLNQGINANGWMRTDLKGSEFTFTPEAPKTI

来源 Source

来源生物 organism	Staphylococcus aureus (strain NCTC 8325 / PS 47)
NCBI Class编号 ncbi_taxonomy_id	93061
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	347

▶

8. Citations (1)

▶

Unit-cell length a length_a	63.210 Å
Unit-cell length b length_b	63.210 Å
Unit-cell length c length_c	273.360 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	16

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	57.370 Å
R factor r_factor	0.1875
R_work r_work	0.1855
R_free r_free	0.2260

fit	/app/data/saxs_computation/sm/7smh/7smh.fit
pddf	/app/data/pr_computation/sm/7smh/7smh.pr.out
profile	/app/data/saxs_computation/sm/7smh/7smh.dat

Structure of SASG A-domain (residues 163-419) from Staphylococcus aureus

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

Surface protein G

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