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1g4w

CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP

Method: X-RAY DIFFRACTION Dmax: 74.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN TYROSINE PHOSPHATASE SPTP

Salmonella typhimurium

UniProt P74873

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 R； UniProt 161–543 Fragment：SPTP RESIDUES 161-543 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；3.5M sodium formate, 2mM DTT, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.20 Å R-free 0.314

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 1G4W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1G4U CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1 Deposited 2000-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 161–543（383 aa） Fragment：SPTP RESIDUES 161-543
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；18 %PEG 400, 0.1M MES, 15mM sodium flouride, 0.1mM aluminum chloride, 2mM DTT, 2mM magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.258
1JYO Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 35–139（105 aa）
Chain F 35–139（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2M sodium chloride, 5-10% polyethylene glycol molecular weight 6000 (PEG6000), supplemented with 2mM DTT and 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.90 Å R-free 0.258

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

View Construct and Data Evidence
UniProt name SPTP_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain R； PDBConstruct 1–383； UniProt 161–543

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 1g4w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1g4w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1g4w
Deposition date deposition_date2000-10-28
Structure title titleCRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP
Keywords keywordsvirulence factor, tyrosine phosphatase, GTPase activating protein, 4-helix bundle, disorder, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.59 Å
Radius of gyration Rg (electron density) rg_electron21.69 Å
Forward intensity I(0) i025722900.00
Molecular weight molecular_weight37914.0 kDa
Excluded volume excluded_volume47220 ų
Envelope volume envelope_volume57039 ų
Hydration-shell volume shell_volume22360 ų
Envelope diameter envelope_diameter76.7 Å
Shell Rg shell_rg28.27 Å
Envelope Rg envelope_rg21.95 Å
Shape Rg shape_rg21.70 Å
Total Rg total_rg22.51 Å
Total atoms total_atoms2656
Residues n_residues341
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 dmax74.6 Å
Rg (real space) rg_real22.59 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real2.5720e+07
I(0) uncertainty (real space) i0_real_error3.6150e+05
Rg (reciprocal space) rg_reciprocal22.59 Å
I(0) (reciprocal space) i0_reciprocal25720000.0000
Solution quality estimate total_estimate0.8862
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.379
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6455000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1g4wr1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.11 — Bacterial GAP domain
Family Family familya.24.11.1 — Bacterial GAP domain
Domain ID domain_idd1g4wr2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamilyc.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family familyc.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (2 domains)

Domain ID domain_id1g4wR01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily260 — Virulence factor YopE uncharacterised domain
Domain ID domain_id1g4wR02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily
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8. Citations (1)

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9. Files and Curves (10)