SAXSdb — 8kge

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tail tube protein

Escherichia phage lambda

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 V； UniProt 1–246 Chain v； UniProt 1–246	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.80 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 8KGE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K4Q The Solution Structure of gpV, the Major Tail Protein from Bacteriophage Lambda Deposited 2008-06-16	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 1–153（153 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 50 mM sodium phosphate, 0.6 mM DSS, 200 mM sodium chloride, 8-10 % D2O, 0.1% % sodium azide, 1 mM [U-100% 13C; U-100% 15N] gpV protein, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] gpV protein, 90-99 % D2O, 0.6 mM DSS, 50 mM sodium phosphate, 200 mM sodium chloride, 0.1 % sodium azide, 90% D2O, 10% H2O \| 90% D2O, 10% H2O	Resolution not provided
2L04 The Solution Structure of the C-terminal Ig-like Domain of the Bacteriophage Lambda Tail Tube Protein Deposited 2010-06-30	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 160–246（87 aa） Fragment：C-terminal, UNP residues 160-246	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) .2；Pressure ambient NMR sample composition 50 mM sodium phosphate-1, 200 mM sodium chloride-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 50 mM sodium phosphate-3, 200 mM sodium chloride-4, 100% D2O \| 100% D2O	Resolution not provided
6P3E Mobile loops and electrostatic interactions maintain the flexible lambda tail tube Deposited 2019-05-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 1–246（246 aa） Chain B 1–246（246 aa） Chain C 1–246（246 aa） Chain D 1–246（246 aa） Chain E 1–246（246 aa） Chain F 1–246（246 aa） Chain G 1–246（246 aa） Chain H 1–246（246 aa） Chain I 1–246（246 aa） Chain J 1–246（246 aa） Chain K 1–246（246 aa） Chain L 1–246（246 aa） Chain M 1–246（246 aa） Chain N 1–246（246 aa） Chain O 1–246（246 aa） Chain P 1–246（246 aa） Chain Q 1–246（246 aa） Chain R 1–246（246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.40 Å
7T2E Structure of bacteriophage lambda tube protein V in C6 Deposited 2021-12-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–157（156 aa） Chain B 2–157（156 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7T4F Structure of bacteriophage lambda tube protein V in C3 Deposited 2021-12-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–246（245 aa） Chain B 2–246（245 aa） Chain C 2–246（245 aa） Chain D 2–246（245 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8IYD Tail cap of phage lambda tail Deposited 2023-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain A 1–246（246 aa） Chain B 1–246（246 aa） Chain C 1–246（246 aa） Chain D 1–246（246 aa） Chain E 1–246（246 aa） Chain F 1–246（246 aa） Chain H 1–246（246 aa） Chain I 1–246（246 aa） Chain J 1–246（246 aa） Chain L 1–246（246 aa） Chain M 1–246（246 aa） Chain N 1–246（246 aa） Chain O 1–246（246 aa） Chain P 1–246（246 aa） Chain R 1–246（246 aa） Chain S 1–246（246 aa） Chain T 1–246（246 aa） Chain V 1–246（246 aa） Chain X 1–246（246 aa） Chain Y 1–246（246 aa） Chain a 1–246（246 aa） Chain b 1–246（246 aa） Chain c 1–246（246 aa） Chain v 1–246（246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
8IYK Tail tip conformation 1 of phage lambda tail Deposited 2023-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A 1–246（246 aa） Chain B 1–246（246 aa） Chain C 1–246（246 aa） Chain D 1–246（246 aa） Chain G 1–246（246 aa） Chain Q 1–246（246 aa） Chain R 1–246（246 aa） Chain S 1–246（246 aa） Chain T 1–246（246 aa） Chain U 1–246（246 aa） Chain V 1–246（246 aa） Chain W 1–246（246 aa） Chain X 1–246（246 aa） Chain a 1–246（246 aa） Chain b 1–246（246 aa） Chain c 1–246（246 aa） Chain d 1–246（246 aa） Chain i 1–246（246 aa） Chain j 1–246（246 aa） Chain k 1–246（246 aa） Chain l 1–246（246 aa） Chain n 1–246（246 aa） Chain o 1–246（246 aa） Chain v 1–246（246 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.95 Å
8IYL Tail tip conformation 2 of phage lambda tail Deposited 2023-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A 1–246（246 aa） Chain B 1–246（246 aa） Chain C 1–246（246 aa） Chain O 1–246（246 aa） Chain P 1–246（246 aa） Chain Q 1–246（246 aa） Chain R 1–246（246 aa） Chain S 1–246（246 aa） Chain T 1–246（246 aa） Chain U 1–246（246 aa） Chain V 1–246（246 aa） Chain W 1–246（246 aa） Chain a 1–246（246 aa） Chain b 1–246（246 aa） Chain c 1–246（246 aa） Chain g 1–246（246 aa） Chain h 1–246（246 aa） Chain i 1–246（246 aa） Chain j 1–246（246 aa） Chain k 1–246（246 aa） Chain l 1–246（246 aa） Chain n 1–246（246 aa） Chain o 1–246（246 aa） Chain v 1–246（246 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8K35 Structure of the bacteriophage lambda tail tip complex Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain L 1–246（246 aa） Chain R 1–246（246 aa） Chain T 1–246（246 aa） Chain U 1–246（246 aa） Chain V 1–246（246 aa） Chain W 1–246（246 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8K36 Structure of the bacteriophage lambda tail tube Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–246（246 aa） Chain B 1–246（246 aa） Chain C 1–246（246 aa） Chain D 1–246（246 aa） Chain E 1–246（246 aa） Chain F 1–246（246 aa） Chain G 1–246（246 aa） Chain H 1–246（246 aa） Chain I 1–246（246 aa） Chain J 1–246（246 aa） Chain K 1–246（246 aa） Chain L 1–246（246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.48 Å
8K37 Structure of the bacteriophage lambda neck Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain G 1–246（246 aa） Chain H 1–246（246 aa） Chain I 1–246（246 aa） Chain J 1–246（246 aa） Chain K 1–246（246 aa） Chain L 1–246（246 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
8XPM Mature virion portal of phage lambda with DNA Deposited 2024-01-04	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain O 1–246（246 aa） Chain O1 1–246（246 aa） Chain O2 1–246（246 aa） Chain P 1–246（246 aa） Chain P1 1–246（246 aa） Chain P2 1–246（246 aa） Chain Q 1–246（246 aa） Chain Q1 1–246（246 aa） Chain Q2 1–246（246 aa） Chain R 1–246（246 aa） Chain R1 1–246（246 aa） Chain R2 1–246（246 aa） Chain V 1–246（246 aa） Chain V1 1–246（246 aa） Chain V2 1–246（246 aa） Chain o 1–246（246 aa） Chain o1 1–246（246 aa） Chain o2 1–246（246 aa） Chain p 1–246（246 aa） Chain p1 1–246（246 aa） Chain p2 1–246（246 aa） Chain q 1–246（246 aa） Chain q1 1–246（246 aa） Chain q2 1–246（246 aa） Chain r 1–246（246 aa） Chain r1 1–246（246 aa） Chain r2 1–246（246 aa） Chain v 1–246（246 aa） Chain v1 1–246（246 aa） Chain v2 1–246（246 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
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Va 3–157（155 aa） Chain Vb 3–157（155 aa） Chain Vc 3–157（155 aa） Chain Vd 3–157（155 aa） Chain Ve 3–157（155 aa） Chain Vf 3–157（155 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TUBE_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain V； PDBConstruct 1–246； UniProt 1–246 Author chain v； PDBConstruct 1–246； UniProt 1–246

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8kge
Deposition date deposition_date	2023-08-18
Structure title title	Dimeric tail tube protein gpVs of bacteriophage lambda
Keywords keywords	Bacteriophage, caudovirales, siphoviridae, tail complex, delivery device, phage lambda, cryo-EM, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.11 Å
Radius of gyration Rg (electron density) rg_electron	28.64 Å
Forward intensity I(0) i0	44720400.00
Molecular weight molecular_weight	50923.0 kDa
Excluded volume excluded_volume	63379 Å³
Envelope volume envelope_volume	86978 Å³
Hydration-shell volume shell_volume	26915 Å³
Envelope diameter envelope_diameter	99.1 Å
Shell Rg shell_rg	33.64 Å
Envelope Rg envelope_rg	29.16 Å
Shape Rg shape_rg	28.63 Å
Total Rg total_rg	29.20 Å
Total atoms total_atoms	3584
Residues n_residues	486
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.5 Å
Rg (real space) rg_real	29.17 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	4.4720e+07
I(0) uncertainty (real space) i0_real_error	6.2850e+05
Rg (reciprocal space) rg_reciprocal	29.15 Å
I(0) (reciprocal space) i0_reciprocal	44720000.0000
Solution quality estimate total_estimate	0.6367
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.492
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6297000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 0.942; 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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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	15620

Description description	Tail tube protein
Molecular weight formula_weight	25831.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,v
Atom count atom_count	3584

Dimeric tail tube protein gpVs of bacteriophage lambda

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tail tube protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia phage lambda
NCBI Class编号 ncbi_taxonomy_id	2681611
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/kg/8kge/8kge.fit
pddf	/app/data/pr_computation/kg/8kge/8kge.pr.out
profile	/app/data/saxs_computation/kg/8kge/8kge.dat