8ovn

X-ray structure of the SF-iGluSnFR-S72A

Method: X-RAY DIFFRACTION Dmax: 77.6 Å Quality: EXCELLENT

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

Putative periplasmic binding transport protein,Green fluorescent protein

Shigella flexneri

UniProt A0A0H2UXX1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 28–276 Chain A; UniProt 279–302 Non-standard monomer:Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.5 M tri-sodium citrate pH 6.5 Resolution 2.60 Å R-free 0.253

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.

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

View Construct and Data Evidence
UniProt name A0A0H2UXX1_SHIFL
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–250; UniProt 28–276 Author chain A; PDBConstruct 495–518; UniProt 279–302

Putative periplasmic binding transport protein,Green fluorescent protein

Shigella flexneri

UniProt P42212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 147–238 Chain A; UniProt 1–148 Non-standard monomer:Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.5 M tri-sodium citrate pH 6.5 Resolution 2.60 Å R-free 0.253

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.

568 other PDB entries and 744 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GFP_AEQVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 251–342; UniProt 147–238 Author chain A; PDBConstruct 349–494; UniProt 1–148

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 8ovn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ovn
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8ovn
Deposition date deposition_date2023-04-26
Structure title titleX-ray structure of the SF-iGluSnFR-S72A
Keywords keywordsaspartate, genetically-encoded biosensor, iAspSnFR, GFP, FLUORESCENT PROTEIN; FLUORESCENT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.65
Radius of gyration Rg (electron density) rg_electron24.67
Forward intensity I(0) i054053600.00
Molecular weight molecular_weight56828.0 kDa
Excluded volume excluded_volume71090 ų
Envelope volume envelope_volume85338 ų
Hydration-shell volume shell_volume28689 ų
Envelope diameter envelope_diameter81.8
Shell Rg shell_rg32.05
Envelope Rg envelope_rg24.72
Shape Rg shape_rg24.63
Total Rg total_rg25.64
Total atoms total_atoms4000
Residues n_residues503
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax77.6
Rg (real space) rg_real25.56
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real5.4050e+07
I(0) uncertainty (real space) i0_real_error7.3280e+05
Rg (reciprocal space) rg_reciprocal25.59
I(0) (reciprocal space) i0_reciprocal54050000.0000
Solution quality estimate total_estimate0.9115
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.597
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14930000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.930

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8ovnA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II

8. Citations (1)

9. Files and Curves (10)