SAXSdb — 8k39

▼

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

Major capsid protein

OrganismNot specified

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 heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain 0； UniProt 1–341 Chain 1； UniProt 1–341 Chain 2； UniProt 1–341 Chain 3； UniProt 1–341 Chain 4； UniProt 1–341 Chain 5； UniProt 1–341 Chain 6； UniProt 1–341 Chain 7； UniProt 1–341 Chain A； UniProt 1–341 Chain B； UniProt 1–341 Chain C； UniProt 1–341 Chain D； UniProt 1–341 Chain E； UniProt 1–341 Chain F； UniProt 1–341 Chain G； UniProt 1–341 Chain H； UniProt 1–341 Chain I； UniProt 1–341 Chain J； UniProt 1–341 Chain K； UniProt 1–341 Chain L； UniProt 1–341 Chain M； UniProt 1–341 Chain N； UniProt 1–341 Chain O； UniProt 1–341 Chain P； UniProt 1–341 Chain Q； UniProt 1–341 Chain R； UniProt 1–341 Chain S； UniProt 1–341 Chain T； UniProt 1–341 Chain g； UniProt 1–341 Chain h； UniProt 1–341	Not recorded	Portal protein B × 12 （P03710）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 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 8K39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SJ5 Bacteriophage lambda major capsid protein mutant - W308A Deposited 2021-10-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa）	Mutation：W308A Mutation：W308A Mutation：W308A Mutation：W308A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291.15 K；0.1 M bis-tris, 0.1 M ammonium sulfate, 5% v/v glycerol, 30% v/v PEG-3350	Resolution 2.69 Å R-free 0.230
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 420 PDB declaration: 420-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 42 PDB declaration: 42-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VIA Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 Angstrom Deposited 2021-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.88 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 840 PDB declaration: 840-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 70 PDB declaration: 70-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VIK Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.76 Å
8XOU Prohead portal vertex of bacteriophage lambda Deposited 2024-01-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A0 1–341（341 aa） Chain A1 1–341（341 aa） Chain A2 1–341（341 aa） Chain A3 1–341（341 aa） Chain A4 1–341（341 aa） Chain C0 1–341（341 aa） Chain C1 1–341（341 aa） Chain C2 1–341（341 aa） Chain C3 1–341（341 aa） Chain C4 1–341（341 aa） Chain D0 1–341（341 aa） Chain D1 1–341（341 aa） Chain D2 1–341（341 aa） Chain D3 1–341（341 aa） Chain D4 1–341（341 aa） Chain E0 1–341（341 aa） Chain E1 1–341（341 aa） Chain E2 1–341（341 aa） Chain E3 1–341（341 aa） Chain E4 1–341（341 aa） Chain F0 1–341（341 aa） Chain F1 1–341（341 aa） Chain F2 1–341（341 aa） Chain F3 1–341（341 aa） Chain F4 1–341（341 aa） Chain G0 1–341（341 aa） Chain G1 1–341（341 aa） Chain G2 1–341（341 aa） Chain G3 1–341（341 aa） Chain G4 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.58 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain A0 1–341（341 aa） Chain A1 1–341（341 aa） Chain A2 1–341（341 aa） Chain A3 1–341（341 aa） Chain A4 1–341（341 aa） Chain C0 1–341（341 aa） Chain C1 1–341（341 aa） Chain C2 1–341（341 aa） Chain C3 1–341（341 aa） Chain C4 1–341（341 aa） Chain G0 1–341（341 aa） Chain G1 1–341（341 aa） Chain G2 1–341（341 aa） Chain G3 1–341（341 aa） Chain G4 1–341（341 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

7 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAPSD_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–341； UniProt 1–341 Author chain 1； PDBConstruct 1–341； UniProt 1–341 Author chain 2； PDBConstruct 1–341； UniProt 1–341 Author chain 3； PDBConstruct 1–341； UniProt 1–341 Author chain 4； PDBConstruct 1–341； UniProt 1–341 Author chain 5； PDBConstruct 1–341； UniProt 1–341 Author chain 6； PDBConstruct 1–341； UniProt 1–341 Author chain 7； PDBConstruct 1–341； UniProt 1–341 Author chain A； PDBConstruct 1–341； UniProt 1–341 Author chain B； PDBConstruct 1–341； UniProt 1–341 Author chain C； PDBConstruct 1–341； UniProt 1–341 Author chain D； PDBConstruct 1–341； UniProt 1–341 Author chain E； PDBConstruct 1–341； UniProt 1–341 Author chain F； PDBConstruct 1–341； UniProt 1–341 Author chain G； PDBConstruct 1–341； UniProt 1–341 Author chain H； PDBConstruct 1–341； UniProt 1–341 Author chain I； PDBConstruct 1–341； UniProt 1–341 Author chain J； PDBConstruct 1–341； UniProt 1–341 Author chain K； PDBConstruct 1–341； UniProt 1–341 Author chain L； PDBConstruct 1–341； UniProt 1–341 Author chain M； PDBConstruct 1–341； UniProt 1–341 Author chain N； PDBConstruct 1–341； UniProt 1–341 Author chain O； PDBConstruct 1–341； UniProt 1–341 Author chain P； PDBConstruct 1–341； UniProt 1–341 Author chain Q； PDBConstruct 1–341； UniProt 1–341 Author chain R； PDBConstruct 1–341； UniProt 1–341 Author chain S； PDBConstruct 1–341； UniProt 1–341 Author chain T； PDBConstruct 1–341； UniProt 1–341 Author chain g； PDBConstruct 1–341； UniProt 1–341 Author chain h； PDBConstruct 1–341； UniProt 1–341

Portal protein B

OrganismNot specified

UniProt P03710

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 heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain U； UniProt 1–533 Chain V； UniProt 1–533 Chain W； UniProt 1–533 Chain X； UniProt 1–533 Chain Y； UniProt 1–533 Chain Z； UniProt 1–533 Chain a； UniProt 1–533 Chain b； UniProt 1–533 Chain c； UniProt 1–533 Chain d； UniProt 1–533 Chain e； UniProt 1–533 Chain f； UniProt 1–533	Not recorded	Major capsid protein × 30 （P03713）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 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 8K39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8K38 The structure of bacteriophage lambda portal-adaptor Deposited 2023-07-14	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–533（533 aa） Chain B 1–533（533 aa） Chain C 1–533（533 aa） Chain D 1–533（533 aa） Chain E 1–533（533 aa） Chain F 1–533（533 aa） Chain G 1–533（533 aa） Chain H 1–533（533 aa） Chain I 1–533（533 aa） Chain J 1–533（533 aa） Chain K 1–533（533 aa） Chain L 1–533（533 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8XOT Prohead portal of bacteriophage lambda Deposited 2024-01-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain B 1–533（533 aa） Chain B1 1–533（533 aa） Chain B2 1–533（533 aa） Chain B3 1–533（533 aa） Chain B4 1–533（533 aa） Chain B5 1–533（533 aa） Chain b 1–533（533 aa） Chain b1 1–533（533 aa） Chain b2 1–533（533 aa） Chain b3 1–533（533 aa） Chain b4 1–533（533 aa） Chain b5 1–533（533 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.51 Å
8XOU Prohead portal vertex of bacteriophage lambda Deposited 2024-01-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain B 1–533（533 aa） Chain B1 1–533（533 aa） Chain B2 1–533（533 aa） Chain B3 1–533（533 aa） Chain B4 1–533（533 aa） Chain B5 1–533（533 aa） Chain b 1–533（533 aa） Chain b1 1–533（533 aa） Chain b2 1–533（533 aa） Chain b3 1–533（533 aa） Chain b4 1–533（533 aa） Chain b5 1–533（533 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.58 Å
8XOW Mature virion portal of bacteriophage lambda Deposited 2024-01-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain B 1–533（533 aa） Chain B1 1–533（533 aa） Chain B2 1–533（533 aa） Chain B3 1–533（533 aa） Chain B4 1–533（533 aa） Chain B5 1–533（533 aa） Chain b 1–533（533 aa） Chain b1 1–533（533 aa） Chain b2 1–533（533 aa） Chain b3 1–533（533 aa） Chain b4 1–533（533 aa） Chain b5 1–533（533 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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain B 1–533（533 aa） Chain B1 1–533（533 aa） Chain B2 1–533（533 aa） Chain B3 1–533（533 aa） Chain B4 1–533（533 aa） Chain B5 1–533（533 aa） Chain b 1–533（533 aa） Chain b1 1–533（533 aa） Chain b2 1–533（533 aa） Chain b3 1–533（533 aa） Chain b4 1–533（533 aa） Chain b5 1–533（533 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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain B 1–533（533 aa） Chain B1 1–533（533 aa） Chain B2 1–533（533 aa） Chain B3 1–533（533 aa） Chain B4 1–533（533 aa） Chain B5 1–533（533 aa） Chain b 1–533（533 aa） Chain b1 1–533（533 aa） Chain b2 1–533（533 aa） Chain b3 1–533（533 aa） Chain b4 1–533（533 aa） Chain b5 1–533（533 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

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PORTL_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–533； UniProt 1–533 Author chain V； PDBConstruct 1–533； UniProt 1–533 Author chain W； PDBConstruct 1–533； UniProt 1–533 Author chain X； PDBConstruct 1–533； UniProt 1–533 Author chain Y； PDBConstruct 1–533； UniProt 1–533 Author chain Z； PDBConstruct 1–533； UniProt 1–533 Author chain a； PDBConstruct 1–533； UniProt 1–533 Author chain b； PDBConstruct 1–533； UniProt 1–533 Author chain c； PDBConstruct 1–533； UniProt 1–533 Author chain d； PDBConstruct 1–533； UniProt 1–533 Author chain e； PDBConstruct 1–533； UniProt 1–533 Author chain f； PDBConstruct 1–533； UniProt 1–533

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8k39
Deposition date deposition_date	2023-07-14
Structure title title	Structure of the bacteriophage lambda portal vertex
Keywords keywords	Complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	107.60 Å
Forward intensity I(0) i0	44810900000.00
Molecular weight molecular_weight	1771900.0 kDa
Excluded volume excluded_volume	2201400 Å³
Envelope volume envelope_volume	4199700 Å³
Hydration-shell volume shell_volume	324400 Å³
Envelope diameter envelope_diameter	364.0 Å
Shell Rg shell_rg	98.44 Å
Envelope Rg envelope_rg	108.10 Å
Shape Rg shape_rg	107.50 Å
Total Rg total_rg	107.60 Å
Total atoms total_atoms	124618
Residues n_residues	15849
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

▼

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

Maximum dimension Dmax dmax	296.9 Å
Rg (real space) rg_real	102.90 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	4.3000e+10
I(0) uncertainty (real space) i0_real_error	9.9690e+08
Rg (reciprocal space) rg_reciprocal	102.90 Å
I(0) (reciprocal space) i0_reciprocal	44230000000.0000
Solution quality estimate total_estimate	0.9120
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	106.0 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.548
Angular range angular_range	— – 0.0700 Å⁻¹
Current regularization parameter α current_alpha	1.1630
Highest regularization parameter α highest_alpha	2029000000.0000
Real-space data points n_real_points	15
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.998; Stabil: 0.966; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Major capsid protein
Molecular weight formula_weight	38229.2 kDa
Source method src_method	nat
Copy count entity_count	30

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0,1,2,3,4,5,6,7,A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,g,h
Atom count atom_count	124618

MSMYTTAQLLAANEQKFKFDPLFLRLFFRESYPFTTEKVYLSQIPGLVNMALYVSPIVSGEVIRSRGGSTSEFTPGYVKPKHEVNPQMTLRRLPDEDPQNLADPAYRRRRIIMQNMRDEELAIAQVEEMQAVSAVLKGKYTMTGEAFDPVEVDMGRSEENNITQSGGTEWSKRDKSTYDPTDDIEAYALNASGVVNIIVFDPKGWALFRSFKAVKEKLDTRRGSNSELETAVKDLGKAVSYKGMYGDVAIVVYSGQYVENGVKKNFLPDNTMVLGNTQARGLRTYGCIQDADAQREGINASARYPKNWVTTGDPAREFTMIQSAPLMLLADPDEFVSVQLA

Entity 2 Entity 2 polymer

Description description	Portal protein B
Molecular weight formula_weight	59529.6 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V,W,X,Y,Z,a,b,c,d,e,f

MKTPTIPTLLGPDGMTSLREYAGYHGGGSGFGGQLRSWNPPSESVDAALLPNFTRGNARADDLVRNNGYAANAIQLHQDHIVGSFFRLSHRPSWRYLGIGEEEARAFSREVEAAWKEFAEDDCCCIDVERKRTFTMMIREGVAMHAFNGELFVQATWDTSSSRLFRTQFRMVSPKRISNPNNTGDSRNCRAGVQINDSGAALGYYVSEDGYPGWMPQKWTWIPRELPGGRASFIHVFEPVEDGQTRGANVFYSVMEQMKMLDTLQNTQLQSAIVKAMYAATIESELDTQSAMDFILGANSQEQRERLTGWIGEIAAYYAAAPVRLGGAKVPHLMPGDSLNLQTAQDTDNGYSVFEQSLLRYIAAGLGVSYEQLSRNYAQMSYSTARASANESWAYFMGRRKFVASRQASQMFLCWLEEAIVRRVVTLPSKARFSFQEARSAWGNCDWIGSGRMAIDGLKEVQEAVMLIEAGLSTYEKECAKRGDDYQEIFAQQVRETMERRAAGLKPPAWAAAAFESGLRQSTEEEKSDSRAA

▶

8. Citations (1)

▶

Resolution resolution	4.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	67924

fit	/app/data/saxs_computation/k3/8k39/8k39.fit
pddf	/app/data/pr_computation/k3/8k39/8k39.pr.out
profile	/app/data/saxs_computation/k3/8k39/8k39.dat

Structure of the bacteriophage lambda portal vertex

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

Major capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

Portal protein B

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)