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3spe

Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ

Method: X-RAY DIFFRACTION Dmax: 101.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ029

Pseudomonas phage phiKZ

UniProt Q8SDD3

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 96–390 Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.286
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 96–390 Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.286
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 96–390 Chain B； UniProt 96–390 Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.286

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 3SPE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J0H Fitting of the bacteriophage phiKZ gp29PR structure into the cryo-EM density map of the phiKZ extended tail sheath Deposited 2011-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane
Resolution 18.00 Å
3J0I Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath Deposited 2011-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane
Resolution 19.00 Å
9XPF The structure of sheath and tube proteins of phage Phikz Deposited 2025-11-16 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 × 24 PDB declaration: 24-meric
Chain A 1–695（695 aa）
Chain B 1–695（695 aa）
Chain C 1–695（695 aa）
Chain D 1–695（695 aa）
Chain E 1–695（695 aa）
Chain F 1–695（695 aa）
Chain M 1–695（695 aa）
Chain N 1–695（695 aa）
Chain O 1–695（695 aa）
Chain P 1–695（695 aa）
Chain Q 1–695（695 aa）
Chain R 1–695（695 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9XPS The neck structure of the Phage Phikz Deposited 2025-11-17 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 × 15 PDB declaration: 15-meric
Chain x 1–695（695 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9XQS Structure of the inner peripheral region in the phage phiKZ baseplate complex Deposited 2025-11-18 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 × 84 PDB declaration: 84-meric
Chain W 1–695（695 aa）
Chain X 1–695（695 aa）
Chain Y 1–695（695 aa）
Chain Z 1–695（695 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8SDD3_BPDPK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–295； UniProt 96–390 Author chain B； PDBConstruct 1–295； UniProt 96–390

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 3spe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3spe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3spe
Deposition date deposition_date2011-07-01
Structure title titleCrystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ
Keywords keywordsStructural Protein; STRUCTURAL 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_guinier29.51 Å
Radius of gyration Rg (electron density) rg_electron29.14 Å
Forward intensity I(0) i051869100.00
Molecular weight molecular_weight55951.0 kDa
Excluded volume excluded_volume69594 ų
Envelope volume envelope_volume84944 ų
Hydration-shell volume shell_volume26611 ų
Envelope diameter envelope_diameter106.3 Å
Shell Rg shell_rg33.44 Å
Envelope Rg envelope_rg29.26 Å
Shape Rg shape_rg29.07 Å
Total Rg total_rg29.80 Å
Total atoms total_atoms3911
Residues n_residues496
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 dmax101.0 Å
Rg (real space) rg_real29.83 Å
Rg uncertainty (real space) rg_real_error0.85 Å
I(0) (real space) i0_real5.1870e+07
I(0) uncertainty (real space) i0_real_error8.1060e+05
Rg (reciprocal space) rg_reciprocal29.70 Å
I(0) (reciprocal space) i0_reciprocal51860000.0000
Solution quality estimate total_estimate0.8059
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.592
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7540000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.671; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.742; Smooth: 0.718
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)