9zw5

Ubiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION Dmax: 75.8 Å Quality: GOOD

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

tRNA threonylcarbamoyladenosine biosynthesis protein TsaE

Porphyromonas gingivalis ATCC 33277

UniProt B2RJJ4

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 1–138 Not recorded MN MANGANESE (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.33;298.15 K;0.1 M Bis Tris propane pH 6.33, 30% polyethylene glycol 3350, 0.2 M Na/K phosphate, 1.25 mM Beryllium sulphate, 8.75 mM Sodium fluoride and 630 mM Manganese chloride Resolution 2.60 Å R-free 0.254
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–138 Not recorded MN MANGANESE (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.33;298.15 K;0.1 M Bis Tris propane pH 6.33, 30% polyethylene glycol 3350, 0.2 M Na/K phosphate, 1.25 mM Beryllium sulphate, 8.75 mM Sodium fluoride and 630 mM Manganese chloride Resolution 2.60 Å R-free 0.254

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 B2RJJ4_PORG3
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–141; UniProt 1–138 Author chain B; PDBConstruct 4–141; UniProt 1–138

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 9zw5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zw5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zw5
Deposition date deposition_date2026-01-01
Structure title titleUbiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis
Keywords keywordsUbiquitous bacterial Kinase, Porohyromonas gingivalis, protein phosphorylation, PorX, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.60
Radius of gyration Rg (electron density) rg_electron21.67
Forward intensity I(0) i018568700.00
Molecular weight molecular_weight32063.0 kDa
Excluded volume excluded_volume39758 ų
Envelope volume envelope_volume48475 ų
Hydration-shell volume shell_volume19502 ų
Envelope diameter envelope_diameter75.6
Shell Rg shell_rg27.25
Envelope Rg envelope_rg21.68
Shape Rg shape_rg21.65
Total Rg total_rg22.46
Total atoms total_atoms2248
Residues n_residues282
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 dmax75.8
Rg (real space) rg_real22.65
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real1.8570e+07
I(0) uncertainty (real space) i0_real_error2.3600e+05
Rg (reciprocal space) rg_reciprocal22.64
I(0) (reciprocal space) i0_reciprocal18570000.0000
Solution quality estimate total_estimate0.8775
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.0
Skewness Skewness skewness0.402
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4709000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)