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8jzl

CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB

Method: ELECTRON MICROSCOPY Dmax: 158.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inositol phosphate phosphatase SopB

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt O30916

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 64–561 Chain B； UniProt 64–561 Chain C； UniProt 64–561 Chain D； UniProt 64–561 Chain E； UniProt 64–561 Chain F； UniProt 64–561 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.62 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 8JZL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4DID Crystal structure of Salmonella effector N-terminal domain SopB in complex with Cdc42 Deposited 2012-01-30 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 × 2 PDB declaration: dimeric
Chain B 30–181（152 aa） Fragment：UNP residues 30-181
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；277 K；0.2M sodium chloride, 0.1M phosphate-citrate pH 4.2, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.35 Å R-free 0.237

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

View Construct and Data Evidence
UniProt name SOPB_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–498； UniProt 64–561 Author chain B； PDBConstruct 1–498； UniProt 64–561 Author chain C； PDBConstruct 1–498； UniProt 64–561 Author chain D； PDBConstruct 1–498； UniProt 64–561 Author chain E； PDBConstruct 1–498； UniProt 64–561 Author chain F； PDBConstruct 1–498； UniProt 64–561

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 8jzl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8jzl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8jzl
Deposition date deposition_date2023-07-05
最后修订 last_revision2024-07-10
Structure title titleCryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB
Keywords keywordsType III secretion system, inositol phosphate phosphatase, bacteria effector, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.22 Å
Radius of gyration Rg (electron density) rg_electron50.51 Å
Forward intensity I(0) i01596170000.00
Molecular weight molecular_weight329540.0 kDa
Excluded volume excluded_volume411440 ų
Envelope volume envelope_volume620550 ų
Hydration-shell volume shell_volume98248 ų
Envelope diameter envelope_diameter156.2 Å
Shell Rg shell_rg58.51 Å
Envelope Rg envelope_rg49.07 Å
Shape Rg shape_rg50.48 Å
Total Rg total_rg50.85 Å
Total atoms total_atoms23184
Residues n_residues2988
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax158.8 Å
Rg (real space) rg_real50.93 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real1.5960e+09
I(0) uncertainty (real space) i0_real_error3.1390e+07
Rg (reciprocal space) rg_reciprocal51.44 Å
I(0) (reciprocal space) i0_reciprocal1597000000.0000
Solution quality estimate total_estimate0.8917
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary71.7 Å
Skewness Skewness skewness-0.031
Kurtosis Kurtosis kurtosis-0.575
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha101900000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.913
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)