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9kyv

The scaffold dimer of phage P22

Method: ELECTRON MICROSCOPY Dmax: 75.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Scaffolding protein

OrganismNot specified

UniProt P26748

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–303 Chain B； UniProt 1–303 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.90 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 9KYV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GP8 NMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACTERIOPHAGE P22 SCAFFOLDING PROTEIN Deposited 1999-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 264–303（40 aa） Fragment：C-TERMINAL FUNCTIONAL DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.4；293 K；Pressure 1
NMR sample composition 10% WATER/90% D2O, 99.9% D2O
Resolution not provided
2GP8 NMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACTERIOPHAGE P22 SCAFFOLDING PROTEIN Deposited 1999-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 264–303（40 aa） Fragment：C-TERMINAL FUNCTIONAL DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.4；293 K；Pressure 1
NMR sample composition 10% WATER/90% D2O, 99.9% D2O
Resolution not provided
8I1V The asymmetric unit of P22 procapsid Deposited 2023-01-13 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 1–303（303 aa）
Chain I 1–303（303 aa）
Chain J 1–303（303 aa）
Chain K 1–303（303 aa）
Chain L 1–303（303 aa）
Chain M 1–303（303 aa）
Chain N 1–303（303 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9KYW The scaffold C-loop of phage P22 Deposited 2024-12-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–303（303 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
9KYX The scaffold tetramer of phage P22 Deposited 2024-12-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–303（303 aa）
Chain B 1–303（303 aa）
Chain C 1–303（303 aa）
Chain D 1–303（303 aa）
Chain E 1–303（303 aa）
Chain F 1–303（303 aa）
Chain G 1–303（303 aa）
Chain H 1–303（303 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å

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

View Construct and Data Evidence
UniProt name VG08_BPP22
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–303； UniProt 1–303 Author chain B； PDBConstruct 1–303； UniProt 1–303

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 9kyv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9kyv
Deposition date deposition_date2024-12-09
Structure title titleThe scaffold dimer of phage P22
Keywords keywordsComplex, 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_guinier23.28 Å
Radius of gyration Rg (electron density) rg_electron22.11 Å
Forward intensity I(0) i015836600.00
Molecular weight molecular_weight28852.0 kDa
Excluded volume excluded_volume35779 ų
Envelope volume envelope_volume47182 ų
Hydration-shell volume shell_volume18510 ų
Envelope diameter envelope_diameter80.2 Å
Shell Rg shell_rg28.03 Å
Envelope Rg envelope_rg22.44 Å
Shape Rg shape_rg22.10 Å
Total Rg total_rg22.96 Å
Total atoms total_atoms2024
Residues n_residues253
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 dmax75.5 Å
Rg (real space) rg_real23.24 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real1.5840e+07
I(0) uncertainty (real space) i0_real_error2.1530e+05
Rg (reciprocal space) rg_reciprocal23.25 Å
I(0) (reciprocal space) i0_reciprocal15840000.0000
Solution quality estimate total_estimate0.8202
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary30.2 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.645
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1899000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.900; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.000
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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)