SAXSdb — 1gw8

▼

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

MAJOR CAPSID PROTEIN

BACTERIOPHAGE PRD1

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 × 720 PDB declaration: 720-MERIC（720） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394 Chain D； UniProt 1–394 Chain E； UniProt 1–394 Chain F； UniProt 1–394 Chain G； UniProt 1–394 Chain H； UniProt 1–394 Chain I； UniProt 1–394 Chain J； UniProt 1–394 Chain K； UniProt 1–394 Chain L； UniProt 1–394	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：TRIS；pH 7.2；TRIS cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE	Resolution 13.30 Å
2	Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394 Chain D； UniProt 1–394 Chain E； UniProt 1–394 Chain F； UniProt 1–394 Chain G； UniProt 1–394 Chain H； UniProt 1–394 Chain I； UniProt 1–394 Chain J； UniProt 1–394 Chain K； UniProt 1–394 Chain L； UniProt 1–394	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：TRIS；pH 7.2；TRIS cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE	Resolution 13.30 Å
3	Protein homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394 Chain D； UniProt 1–394 Chain E； UniProt 1–394 Chain F； UniProt 1–394 Chain G； UniProt 1–394 Chain H； UniProt 1–394 Chain I； UniProt 1–394 Chain J； UniProt 1–394 Chain K； UniProt 1–394 Chain L； UniProt 1–394	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：TRIS；pH 7.2；TRIS cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE	Resolution 13.30 Å
4	Protein homooligomer Homooligomer Protein × 72 PDB declaration: 72-meric（72） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394 Chain D； UniProt 1–394 Chain E； UniProt 1–394 Chain F； UniProt 1–394 Chain G； UniProt 1–394 Chain H； UniProt 1–394 Chain I； UniProt 1–394 Chain J； UniProt 1–394 Chain K； UniProt 1–394 Chain L； UniProt 1–394	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：TRIS；pH 7.2；TRIS cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE	Resolution 13.30 Å
5	Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394 Chain D； UniProt 1–394 Chain E； UniProt 1–394 Chain F； UniProt 1–394 Chain G； UniProt 1–394 Chain H； UniProt 1–394 Chain I； UniProt 1–394 Chain J； UniProt 1–394 Chain K； UniProt 1–394 Chain L； UniProt 1–394	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：TRIS；pH 7.2；TRIS cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE	Resolution 13.30 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 1GW8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJD THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON Deposited 1999-04-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；35% (W/V) MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.2	Resolution 1.85 Å R-free 0.205
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 540 PDB declaration: 540-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 45 PDB declaration: 45-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 54 PDB declaration: 54-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HQN THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1. Deposited 2000-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；30% MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.227
1HX6 P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1. Deposited 2001-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 7 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；30% MPD, 0.1 M sodium acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.208
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 900 PDB declaration: 900-MERIC	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 75 PDB declaration: 75-meric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 90 PDB declaration: 90-meric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
1W8X Structural analysis of PRD1 Deposited 2004-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 900 PDB declaration: 900-meric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa） Chain D 1–395（395 aa） Chain E 1–395（395 aa） Chain F 1–395（395 aa） Chain G 1–395（395 aa） Chain H 1–395（395 aa） Chain I 1–395（395 aa） Chain J 1–395（395 aa） Chain K 1–395（395 aa） Chain L 1–395（395 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
7OOK Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ Deposited 2021-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa）	Not recorded	NA SODIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；please see: PMID: 10499799	Resolution 2.23 Å R-free 0.216

9 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COA3_BPPRD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394 Author chain C； PDBConstruct 1–394； UniProt 1–394 Author chain D； PDBConstruct 1–394； UniProt 1–394 Author chain E； PDBConstruct 1–394； UniProt 1–394 Author chain F； PDBConstruct 1–394； UniProt 1–394 Author chain G； PDBConstruct 1–394； UniProt 1–394 Author chain H； PDBConstruct 1–394； UniProt 1–394 Author chain I； PDBConstruct 1–394； UniProt 1–394 Author chain J； PDBConstruct 1–394； UniProt 1–394 Author chain K； PDBConstruct 1–394； UniProt 1–394 Author chain L； PDBConstruct 1–394； UniProt 1–394

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	1gw8
Deposition date deposition_date	2002-03-08
Structure title title	quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography.
Keywords keywords	;VIRUS/VIRAL PROTEIN, TECTIVIRIDAE, BACTERIOPHAGE PRD1, CRYO- EM, IMAGE RECONSTRUCTION, ICOSAHEDRAL VIRUS, VIRUS-VIRAL PROTEIN complex ;; VIRUS/VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	58.25 Å
Radius of gyration Rg (electron density) rg_electron	58.16 Å
Forward intensity I(0) i0	3295880000.00
Molecular weight molecular_weight	483350.0 kDa
Excluded volume excluded_volume	604030 Å³
Envelope volume envelope_volume	831110 Å³
Hydration-shell volume shell_volume	118020 Å³
Envelope diameter envelope_diameter	210.1 Å
Shell Rg shell_rg	60.53 Å
Envelope Rg envelope_rg	57.66 Å
Shape Rg shape_rg	58.16 Å
Total Rg total_rg	58.21 Å
Total atoms total_atoms	34170
Residues n_residues	4464
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	187.9 Å
Rg (real space) rg_real	58.40 Å
Rg uncertainty (real space) rg_real_error	1.49 Å
I(0) (real space) i0_real	3.2960e+09
I(0) uncertainty (real space) i0_real_error	6.4800e+07
Rg (reciprocal space) rg_reciprocal	58.11 Å
I(0) (reciprocal space) i0_reciprocal	3294000000.0000
Solution quality estimate total_estimate	0.8431
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	62.6 Å
Skewness Skewness skewness	0.427
Kurtosis Kurtosis kurtosis	-0.222
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	764400000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.276

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1gw8a_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8b_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8c_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8d_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8e_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8f_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8g_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8h_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8i_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8j_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8k_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1gw8l_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

▶

8. Citations (4)

▶

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	1

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

Resolution resolution	13.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	13.30 Å
Resolution测定方法 resolution_method	POLAR FOURIER TRANSFORM, CROSS- COMMON LINES
颗粒数 num_particles	1729

Description description	MAJOR CAPSID PROTEIN
Molecular weight formula_weight	43346.2 kDa
Source method src_method	man
Copy count entity_count	12

quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography.

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

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	34170

来源生物 organism	BACTERIOPHAGE PRD1
NCBI Class编号 ncbi_taxonomy_id	10658
宿主生物 host_organism	SALMONELLA TYPHIMURIUM

fit	/app/data/saxs_computation/gw/1gw8/1gw8.fit
pddf	/app/data/pr_computation/gw/1gw8/1gw8.pr.out
profile	/app/data/saxs_computation/gw/1gw8/1gw8.dat