1cjd

THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON

Method: X-RAY DIFFRACTION D_max: 90.2 Å Quality: EXCELLENT

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

PROTEIN (MAJOR CAPSID PROTEIN (P3))

Enterobacteria phage 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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394 Chain C； UniProt 1–394	Not recorded	No other associated polymer	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

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 1CJD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 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 method 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 method 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 method 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 method 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 method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 mutation/modification 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 ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 ligand/ion 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 34 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

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cjd
Deposition date deposition_date	1999-04-12
Structure title title	THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON
Keywords keywords	BACTERIOPHAGE PRD1, COAT PROTEIN, JELLY ROLL, Viral protein; VIRAL PROTEIN
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	31.39 Å
Radius of gyration Rg (electron density) rg_electron	29.99 Å
Forward intensity I(0) i0	229417000.00
Molecular weight molecular_weight	120260.0 kDa
Excluded volume excluded_volume	150240 Å³
Envelope volume envelope_volume	184480 Å³
Hydration-shell volume shell_volume	48579 Å³
Envelope diameter envelope_diameter	94.7 Å
Shell Rg shell_rg	39.33 Å
Envelope Rg envelope_rg	29.64 Å
Shape Rg shape_rg	29.99 Å
Total Rg total_rg	30.81 Å
Total atoms total_atoms	8502
Residues n_residues	1108
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	90.2 Å
Rg (real space) rg_real	31.10 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	2.2940e+08
I(0) uncertainty (real space) i0_real_error	3.1400e+06
Rg (reciprocal space) rg_reciprocal	31.23 Å
I(0) (reciprocal space) i0_reciprocal	229400000.0000
Solution quality estimate total_estimate	0.9094
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	-0.018
Kurtosis Kurtosis kurtosis	-0.619
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29040000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1cjda1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

Domain ID domain_id	d1cjda2
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

Domain ID domain_id	d1cjdb1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

Domain ID domain_id	d1cjdb2
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

Domain ID domain_id	d1cjdc1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

Domain ID domain_id	d1cjdc2
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.2 — Group II dsDNA viruses VP
Family Family family	b.121.2.1 — Coat protein p3

CATH v4.4 (6 domains)

Domain ID domain_id	1cjdA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	9 — Adenovirus Type 2 Hexon; domain 4
Homologous superfamily homologous superfamily	30 — Viral coat protein p3

Domain ID domain_id	1cjdA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1cjdB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	9 — Adenovirus Type 2 Hexon; domain 4
Homologous superfamily homologous superfamily	30 — Viral coat protein p3

Domain ID domain_id	1cjdB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1cjdC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	9 — Adenovirus Type 2 Hexon; domain 4
Homologous superfamily homologous superfamily	30 — Viral coat protein p3

Domain ID domain_id	1cjdC02
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 (3)

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Unit-cell length a length_a	117.956 Å
Unit-cell length b length_b	121.296 Å
Unit-cell length c length_c	126.387 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.2050

Description description	PROTEIN (MAJOR CAPSID PROTEIN (P3))
Molecular weight formula_weight	43346.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8975

THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON

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

PROTEIN (MAJOR CAPSID PROTEIN (P3))

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Enterobacteria phage PRD1
NCBI Class编号 ncbi_taxonomy_id	10658
宿主生物 host_organism	Salmonella typhimurium

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	473

fit	/app/data/saxs_computation/cj/1cjd/1cjd.fit
pddf	/app/data/pr_computation/cj/1cjd/1cjd.pr.out
profile	/app/data/saxs_computation/cj/1cjd/1cjd.dat