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9xpg

The structure of gp139 protein of phage phikz

Method: ELECTRON MICROSCOPY Dmax: 141.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ139

OrganismNot specified

UniProt Q8SD23

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–298 Chain B； UniProt 1–298 Chain C； UniProt 1–298 Chain D； UniProt 1–298 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.14 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.

Other PDB Difference from Current Entry 9XPG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9XQD The structure of outer peripheral region in the phage phiKZ baseplate complex Deposited 2025-11-18 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain 1 1–298（298 aa）
Chain 2 1–298（298 aa）
Chain 3 1–298（298 aa）
Chain 4 1–298（298 aa）
Chain 5 1–298（298 aa）
Chain 6 1–298（298 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å

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

View Construct and Data Evidence
UniProt name Q8SD23_BPDPK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–298； UniProt 1–298 Author chain B； PDBConstruct 1–298； UniProt 1–298 Author chain C； PDBConstruct 1–298； UniProt 1–298 Author chain D； PDBConstruct 1–298； UniProt 1–298

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 9xpg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xpg
Deposition date deposition_date2025-11-16
Structure title titleThe structure of gp139 protein of phage phikz
Keywords keywordsbaseplate, inner peripheral, 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_guinier42.35 Å
Radius of gyration Rg (electron density) rg_electron42.46 Å
Forward intensity I(0) i0207224000.00
Molecular weight molecular_weight117270.0 kDa
Excluded volume excluded_volume147160 ų
Envelope volume envelope_volume214480 ų
Hydration-shell volume shell_volume45010 ų
Envelope diameter envelope_diameter157.2 Å
Shell Rg shell_rg43.52 Å
Envelope Rg envelope_rg42.20 Å
Shape Rg shape_rg42.48 Å
Total Rg total_rg42.47 Å
Total atoms total_atoms8267
Residues n_residues1068
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 dmax141.7 Å
Rg (real space) rg_real42.74 Å
Rg uncertainty (real space) rg_real_error1.47 Å
I(0) (real space) i0_real2.0720e+08
I(0) uncertainty (real space) i0_real_error3.8160e+06
Rg (reciprocal space) rg_reciprocal42.35 Å
I(0) (reciprocal space) i0_reciprocal207100000.0000
Solution quality estimate total_estimate0.8129
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.3 Å
Skewness Skewness skewness0.550
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38110000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.280
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)