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9xpe

Structure of the Portal and Adaptor Proteins of the Phage Phikz

Method: ELECTRON MICROSCOPY Dmax: 192.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ042

OrganismNot specified

UniProt Q8SDC0

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain A； UniProt 1–266 Chain B； UniProt 1–266 Chain C； UniProt 1–266 Chain D； UniProt 1–266 Chain E； UniProt 1–266 Chain F； UniProt 1–266 Chain G； UniProt 1–266 Chain H； UniProt 1–266 Chain I； UniProt 1–266 Chain J； UniProt 1–266 Chain K； UniProt 1–266 Chain L； UniProt 1–266 Not recorded PHIKZ129 × 12 （Q8SD33） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.37 Å

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 Q8SDC0_BPDPK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–266； UniProt 1–266 Author chain B； PDBConstruct 1–266； UniProt 1–266 Author chain C； PDBConstruct 1–266； UniProt 1–266 Author chain D； PDBConstruct 1–266； UniProt 1–266 Author chain E； PDBConstruct 1–266； UniProt 1–266 Author chain F； PDBConstruct 1–266； UniProt 1–266 Author chain G； PDBConstruct 1–266； UniProt 1–266 Author chain H； PDBConstruct 1–266； UniProt 1–266 Author chain I； PDBConstruct 1–266； UniProt 1–266 Author chain J； PDBConstruct 1–266； UniProt 1–266 Author chain K； PDBConstruct 1–266； UniProt 1–266 Author chain L； PDBConstruct 1–266； UniProt 1–266

PHIKZ129

OrganismNot specified

UniProt Q8SD33

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain M； UniProt 1–896 Chain N； UniProt 1–896 Chain O； UniProt 1–896 Chain P； UniProt 1–896 Chain Q； UniProt 1–896 Chain R； UniProt 1–896 Chain S； UniProt 1–896 Chain T； UniProt 1–896 Chain U； UniProt 1–896 Chain V； UniProt 1–896 Chain W； UniProt 1–896 Chain X； UniProt 1–896 Not recorded PHIKZ042 × 12 （Q8SDC0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.37 Å

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 Q8SD33_BPDPK
Isoform —
PDB entities 2
Chains and sequence ranges Author chain M； PDBConstruct 1–896； UniProt 1–896 Author chain N； PDBConstruct 1–896； UniProt 1–896 Author chain O； PDBConstruct 1–896； UniProt 1–896 Author chain P； PDBConstruct 1–896； UniProt 1–896 Author chain Q； PDBConstruct 1–896； UniProt 1–896 Author chain R； PDBConstruct 1–896； UniProt 1–896 Author chain S； PDBConstruct 1–896； UniProt 1–896 Author chain T； PDBConstruct 1–896； UniProt 1–896 Author chain U； PDBConstruct 1–896； UniProt 1–896 Author chain V； PDBConstruct 1–896； UniProt 1–896 Author chain W； PDBConstruct 1–896； UniProt 1–896 Author chain X； PDBConstruct 1–896； UniProt 1–896

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 9xpe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xpe
Deposition date deposition_date2025-11-16
Structure title titleStructure of the Portal and Adaptor Proteins of the Phage Phikz
Keywords keywordsportal, adaptor, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier73.40 Å
Radius of gyration Rg (electron density) rg_electron73.08 Å
Forward intensity I(0) i018611900000.00
Molecular weight molecular_weight1173000.0 kDa
Excluded volume excluded_volume1472300 ų
Envelope volume envelope_volume2449100 ų
Hydration-shell volume shell_volume258930 ų
Envelope diameter envelope_diameter207.0 Å
Shell Rg shell_rg87.34 Å
Envelope Rg envelope_rg70.05 Å
Shape Rg shape_rg73.11 Å
Total Rg total_rg73.12 Å
Total atoms total_atoms82512
Residues n_residues10284
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 dmax192.7 Å
Rg (real space) rg_real72.93 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.8610e+10
I(0) uncertainty (real space) i0_real_error3.5080e+08
Rg (reciprocal space) rg_reciprocal74.93 Å
I(0) (reciprocal space) i0_reciprocal18690000000.0000
Solution quality estimate total_estimate0.8451
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary100.9 Å
Skewness Skewness skewness-0.098
Kurtosis Kurtosis kurtosis-0.589
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha1661000000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.995; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
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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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8. Citations (1)

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9. Files and Curves (10)