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2gp8

NMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACTERIOPHAGE P22 SCAFFOLDING PROTEIN

Method: SOLUTION NMR Dmax: 42.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (SCAFFOLDING PROTEIN)

Enterobacteria phage P22

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 264–303 Fragment：C-TERMINAL FUNCTIONAL DOMAIN No other associated polymer 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

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 2GP8 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 Parsed fields agree 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 experimental method Different experimental conditions 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
9KYV The scaffold dimer of phage P22 Deposited 2024-12-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–303（303 aa）
Chain B 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 4.90 Å
9KYW The scaffold C-loop of phage P22 Deposited 2024-12-09 Different construct Different oligomeric state Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 1–40； UniProt 264–303

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 2gp8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gp8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gp8
Deposition date deposition_date1999-05-11
Structure title titleNMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACTERIOPHAGE P22 SCAFFOLDING PROTEIN
Keywords keywordsSCAFFOLDING PROTEIN, COAT PROTEIN-BINDING DOMAIN, HELIX-LOOP-HELIX MOTIF, Viral protein; VIRAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.19 Å
Radius of gyration Rg (electron density) rg_electron11.03 Å
Forward intensity I(0) i0536628.00
Molecular weight molecular_weight4324.0 kDa
Excluded volume excluded_volume5419 ų
Envelope volume envelope_volume6607 ų
Hydration-shell volume shell_volume5826 ų
Envelope diameter envelope_diameter39.6 Å
Shell Rg shell_rg15.10 Å
Envelope Rg envelope_rg11.58 Å
Shape Rg shape_rg11.00 Å
Total Rg total_rg12.47 Å
Total atoms total_atoms629
Residues n_residues40
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 dmax42.8 Å
Rg (real space) rg_real12.23 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real5.3660e+05
I(0) uncertainty (real space) i0_real_error5.8890e+03
Rg (reciprocal space) rg_reciprocal12.23 Å
I(0) (reciprocal space) i0_reciprocal536600.0000
Solution quality estimate total_estimate0.7153
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.3 Å
Skewness Skewness skewness0.353
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55570.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 0.368; Positv: 1.000; Valcen: 0.880; Smooth: 0.959
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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2gp8a_
Class classj — Peptides
Fold Fold foldj.58 — Coat protein-binding domain of bacteriophage P22 scaffolding protein
Superfamily Superfamily superfamilyj.58.1 — Coat protein-binding domain of bacteriophage P22 scaffolding protein
Family Family familyj.58.1.1 — Coat protein-binding domain of bacteriophage P22 scaffolding protein

CATH v4.4 (1 domains)

Domain ID domain_id2gp8A00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology810 — Virus Scaffolding Protein; Chain A
Homologous superfamily homologous superfamily10 — Virus Scaffolding Protein; Chain A
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8. Citations (1)

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9. Files and Curves (10)