SAXSdb — 1m06

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

Capsid Protein

Enterobacteria phage alpha3

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–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 60 （P31281） Small core protein × 60 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
2	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 1 （P31281） Small core protein × 1 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
3	Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 5 （P31281） Small core protein × 5 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
4	Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 6 （P31281） Small core protein × 6 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
5	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 1 （P31281） Small core protein × 1 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
6	Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-meric（240） Consistent with all polymer counts	Chain F； UniProt 1–431	Not recorded	Major spike protein × 60 （P31281） Small core protein × 60 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234

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 1M06	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC	Chain F 1–431（431 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–431（431 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain F 1–431（431 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain F 1–431（431 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–431（431 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–DNA Heteromer；Protein × 60 PDB declaration: 80-meric	Chain F 1–431（431 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 120	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGF_BPAL3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 1–431； UniProt 1–431

Major spike protein

Enterobacteria phage alpha3

UniProt P31281

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–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 60 （P08767） Small core protein × 60 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
2	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 1 （P08767） Small core protein × 1 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
3	Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 5 （P08767） Small core protein × 5 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
4	Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 6 （P08767） Small core protein × 6 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
5	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 1 （P08767） Small core protein × 1 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
6	Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-meric（240） Consistent with all polymer counts	Chain G； UniProt 1–187	Not recorded	Capsid Protein × 60 （P08767） Small core protein × 60 （P08766） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234

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 1M06	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC	Chain G 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain G 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain G 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA	Resolution 16.00 Å
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–DNA Heteromer；Protein × 60 PDB declaration: 80-meric	Chain G 1–187（187 aa）	Not recorded	DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 120	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.236

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGG_BPAL3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–187； UniProt 1–187

Small core protein

Enterobacteria phage alpha3

UniProt P08766

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–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 60 （P08767） Major spike protein × 60 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
2	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 1 （P08767） Major spike protein × 1 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
3	Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 5 （P08767） Major spike protein × 5 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
4	Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 6 （P08767） Major spike protein × 6 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
5	Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 1 （P08767） Major spike protein × 1 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234
6	Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-meric（240） Consistent with all polymer counts	Chain J； UniProt 1–24	Not recorded	Capsid Protein × 60 （P08767） Major spike protein × 60 （P31281） 5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3' × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K	Resolution 3.50 Å R-free 0.234

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	VGJ_BPAL3
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–24； UniProt 1–24

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	1m06
Deposition date deposition_date	2002-06-12
Structure title title	Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography
Keywords keywords	;Bacteriophage, three-dimensional structure, virion, morphogenesis, phiX174, assembly, microviridae, Icosahedral virus, Virus-DNA COMPLEX ;; Virus/DNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.17 Å
Radius of gyration Rg (electron density) rg_electron	30.83 Å
Forward intensity I(0) i0	89569900.00
Molecular weight molecular_weight	72507.0 kDa
Excluded volume excluded_volume	89740 Å³
Envelope volume envelope_volume	119570 Å³
Hydration-shell volume shell_volume	33611 Å³
Envelope diameter envelope_diameter	111.0 Å
Shell Rg shell_rg	36.19 Å
Envelope Rg envelope_rg	31.38 Å
Shape Rg shape_rg	30.78 Å
Total Rg total_rg	31.47 Å
Total atoms total_atoms	5093
Residues n_residues	633
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	104.5 Å
Rg (real space) rg_real	31.27 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	8.9570e+07
I(0) uncertainty (real space) i0_real_error	1.4170e+06
Rg (reciprocal space) rg_reciprocal	31.23 Å
I(0) (reciprocal space) i0_reciprocal	89570000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.404
Kurtosis Kurtosis kurtosis	-0.359
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12850000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.918

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Capsid Protein
Molecular weight formula_weight	49294.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	5093

MSNVQTSAEREIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLAIDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRIPKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYGFRCCHLKNIWSAPLPPETKLAEEMGIESNSIDIMGLQAAYAQLHTEQERTYFMQRYRDVISSFGGSTSYDADNRPLLVMHTDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEHHYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVNFKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRHMPTVRDSIMTS

来源 Source

来源生物 organism	Enterobacteria phage alpha3
NCBI Class编号 ncbi_taxonomy_id	10849
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Major spike protein
Molecular weight formula_weight	19599.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK

来源 Source

来源生物 organism	Enterobacteria phage alpha3
NCBI Class编号 ncbi_taxonomy_id	10849

Entity 3 Entity 3 polymer

Description description	Small core protein
Molecular weight formula_weight	2831.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MKKARRSPSRRKGARLWYVGGSQF

来源 Source

来源生物 organism	Enterobacteria phage alpha3
NCBI Class编号 ncbi_taxonomy_id	10849

Entity 4 Entity 4 polymer

Description description	5'-D(P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR)P(3DR))-3'
Molecular weight formula_weight	1756.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

NNNNNNNNNN

来源 Source

来源生物 organism	Enterobacteria phage alpha3
NCBI Class编号 ncbi_taxonomy_id	10849

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m06f_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.1 — Microviridae-like VP

Domain ID domain_id	d1m06g_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.1 — Microviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id	1m06F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	169 — Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
Homologous superfamily homologous superfamily	10 — Microviridae F protein

Domain ID domain_id	1m06G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	290.258 Å
Unit-cell length b length_b	332.115 Å
Unit-cell length c length_c	337.698 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	82.450 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2340

fit	/app/data/saxs_computation/m0/1m06/1m06.fit
pddf	/app/data/pr_computation/m0/1m06/1m06.pr.out
profile	/app/data/saxs_computation/m0/1m06/1m06.dat

Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography

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

Capsid Protein

State in the Current Structure

Other States of the Same Protein in the Database

Major spike protein

State in the Current Structure

Other States of the Same Protein in the Database

Small core 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)