1k46

Crystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer

Method: X-RAY DIFFRACTION Dmax: 62.8 Å Quality: GOOD

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

PROTEIN-TYROSINE PHOSPHATASE YOPH

Yersinia pseudotuberculosis

UniProt P08538

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 1–129 Fragment:amino-terminal domain (residues 1-129) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;PEG 8000, sodium chlolride, Tris , VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.20 Å R-free 0.257
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–129 Fragment:amino-terminal domain (residues 1-129) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;PEG 8000, sodium chlolride, Tris , VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.20 Å R-free 0.257

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name YOPH_YERPS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 1–129

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 1k46

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k46
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k46
Deposition date deposition_date2001-10-05
Structure title titleCrystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer
Keywords keywordsdomain-swap, phosphopeptide-binding domain, type III secretion domain, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.99
Radius of gyration Rg (electron density) rg_electron16.87
Forward intensity I(0) i04064150.00
Molecular weight molecular_weight13460.0 kDa
Excluded volume excluded_volume16611 ų
Envelope volume envelope_volume21356 ų
Hydration-shell volume shell_volume11757 ų
Envelope diameter envelope_diameter64.2
Shell Rg shell_rg21.27
Envelope Rg envelope_rg17.19
Shape Rg shape_rg16.86
Total Rg total_rg17.80
Total atoms total_atoms944
Residues n_residues124
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 dmax62.8
Rg (real space) rg_real18.10
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real4.0640e+06
I(0) uncertainty (real space) i0_real_error5.4540e+04
Rg (reciprocal space) rg_reciprocal18.09
I(0) (reciprocal space) i0_reciprocal4064000.0000
Solution quality estimate total_estimate0.7781
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary56.0
Skewness Skewness skewness0.462
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.4400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha529300.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.742; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1k46a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.195 — YopH tyrosine phosphatase N-terminal domain
Superfamily Superfamily superfamilyd.195.1 — YopH tyrosine phosphatase N-terminal domain
Family Family familyd.195.1.1 — YopH tyrosine phosphatase N-terminal domain

CATH v4.4 (1 domains)

Domain ID domain_id1k46A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1570 — YopH tyrosine phosphatase N-terminal domain
Homologous superfamily homologous superfamily10 — Protein-tyrosine phosphatase, YopH, N-terminal domain

8. Citations (3)

9. Files and Curves (10)