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2kx4

Solution structure of Bacteriophage Lambda gpFII

Method: SOLUTION NMR Dmax: 54.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tail attachment protein

Bacteriophage lambda

UniProt P03714

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 1–117 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：1.5 mM [U-100% 13C; U-100% 15N] gpFII, 90% H2O/10% D2O | 90% H2O/10% 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 2KX4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1K0H Solution structure of bacteriophage lambda gpFII Deposited 2001-09-19 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–117（117 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 200mM NaCl；Pressure ambient
NMR sample composition 1.3mM gpFII U-15N, 13C; 10MM PHOSPHATE BUFFER NA, 200MM NACL | 90% H2O/10% D2O
Resolution not provided
8K37 Structure of the bacteriophage lambda neck Deposited 2023-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain M 1–117（117 aa）
Chain N 1–117（117 aa）
Chain O 1–117（117 aa）
Chain P 1–117（117 aa）
Chain Q 1–117（117 aa）
Chain R 1–117（117 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8XOW Mature virion portal of bacteriophage lambda Deposited 2024-01-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain f 1–117（117 aa）
Chain f1 1–117（117 aa）
Chain f2 1–117（117 aa）
Chain f3 1–117（117 aa）
Chain f4 1–117（117 aa）
Chain f5 1–117（117 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.32 Å
8XPM Mature virion portal of phage lambda with DNA Deposited 2024-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 66 PDB declaration: 68-meric
Chain f 1–117（117 aa）
Chain f1 1–117（117 aa）
Chain f2 1–117（117 aa）
Chain f3 1–117（117 aa）
Chain f4 1–117（117 aa）
Chain f5 1–117（117 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.90 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric
Chain f 1–117（117 aa）
Chain f1 1–117（117 aa）
Chain f2 1–117（117 aa）
Chain f3 1–117（117 aa）
Chain f4 1–117（117 aa）
Chain f5 1–117（117 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 4.07 Å

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

View Construct and Data Evidence
UniProt name VCF2_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–117； UniProt 1–117

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 2kx4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kx4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kx4
Deposition date deposition_date2010-04-26
Structure title titleSolution structure of Bacteriophage Lambda gpFII
Keywords keywords;gpFII, connector protein, Structural Genomics, PSI, Protein Structure Initiative, Ontario Centre for Structural Proteomics, OCSP, 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_guinier20.21 Å
Radius of gyration Rg (electron density) rg_electron20.21 Å
Forward intensity I(0) i0276362000.00
Molecular weight molecular_weight127390.0 kDa
Excluded volume excluded_volume155430 ų
Envelope volume envelope_volume87634 ų
Hydration-shell volume shell_volume27024 ų
Envelope diameter envelope_diameter117.5 Å
Shell Rg shell_rg32.99 Å
Envelope Rg envelope_rg31.90 Å
Shape Rg shape_rg20.15 Å
Total Rg total_rg21.02 Å
Total atoms total_atoms17510
Residues n_residues1170
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 dmax54.5 Å
Rg (real space) rg_real18.10 Å
Rg uncertainty (real space) rg_real_error0.13 Å
I(0) (real space) i0_real2.6140e+08
I(0) uncertainty (real space) i0_real_error2.4460e+06
Rg (reciprocal space) rg_reciprocal20.75 Å
I(0) (reciprocal space) i0_reciprocal276300000.0000
Solution quality estimate total_estimate0.6687
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.7 Å
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis-0.278
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha1.7830
Highest regularization parameter α highest_alpha1066000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.917; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.972; 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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2kx4a_
Class classb — All beta proteins
Fold Fold foldb.106 — Phage tail proteins
Superfamily Superfamily superfamilyb.106.1 — Phage tail proteins
Family Family familyb.106.1.2 — gpFII-like

CATH v4.4 (1 domains)

Domain ID domain_id2kx4A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily180 — Phage tail proteins
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8. Citations (1)

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9. Files and Curves (10)