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2h7o

Crystal structure of the Rho-GTPase binding domain of YpkA

Method: X-RAY DIFFRACTION Dmax: 100.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein kinase ypkA

Yersinia pseudotuberculosis

UniProt Q05608

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 434–732 Fragment：C-terminal Domain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.5；276 K；100mM CAPs pH 10.5, 140mM-180mM NaCl, 16%-18% PEG1500 Micro Seeding, VAPOR DIFFUSION, HANGING DROP, temperature 276K Resolution 2.00 Å R-free 0.237

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 2H7O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2H7V Co-crystal structure of YpkA-Rac1 Deposited 2006-06-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 434–732（299 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.60 Å R-free 0.257
2H7V Co-crystal structure of YpkA-Rac1 Deposited 2006-06-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 434–732（299 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.60 Å R-free 0.257

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

View Construct and Data Evidence
UniProt name YPKA_YERPS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–303； UniProt 434–732

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 2h7o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2h7o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2h7o
Deposition date deposition_date2006-06-02
Structure title titleCrystal structure of the Rho-GTPase binding domain of YpkA
Keywords keywordsYpkA, YopO, Yersinia, GDI, 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_guinier27.52 Å
Radius of gyration Rg (electron density) rg_electron27.72 Å
Forward intensity I(0) i016796700.00
Molecular weight molecular_weight30865.0 kDa
Excluded volume excluded_volume38647 ų
Envelope volume envelope_volume51259 ų
Hydration-shell volume shell_volume17727 ų
Envelope diameter envelope_diameter105.0 Å
Shell Rg shell_rg30.39 Å
Envelope Rg envelope_rg28.00 Å
Shape Rg shape_rg27.73 Å
Total Rg total_rg28.01 Å
Total atoms total_atoms2169
Residues n_residues270
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 dmax100.2 Å
Rg (real space) rg_real28.02 Å
Rg uncertainty (real space) rg_real_error1.36 Å
I(0) (real space) i0_real1.6800e+07
I(0) uncertainty (real space) i0_real_error2.8890e+05
Rg (reciprocal space) rg_reciprocal27.87 Å
I(0) (reciprocal space) i0_reciprocal16790000.0000
Solution quality estimate total_estimate0.7548
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4 Å
Skewness Skewness skewness0.605
Kurtosis Kurtosis kurtosis-0.341
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2327000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.519; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.310; Smooth: 0.940
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2h7oA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1330 — Rac1-binding domain, N-terminal GTPase binding subdomain
Domain ID domain_id2h7oA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1230 — Rac1-binding domain, C-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)