SAXSdb — 6p22

▼

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

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 484–565 Chain B； UniProt 484–565 Chain C； UniProt 484–565	Not recorded	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN × 1 （Q7N648） MG MAGNESIUM ION × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0	Resolution 2.29 Å R-free 0.222

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 6P22	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1K28 The Structure of the Bacteriophage T4 Cell-Puncturing Device Deposited 2001-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–575（575 aa）	Not recorded	K POTASSIUM ION × 3 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；279 K；PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.90 Å R-free 0.280
1PDL Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate Deposited 2003-05-19	Different construct 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 1–575（575 aa） Chain B 1–575（575 aa） Chain C 1–575（575 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer water；pH 7；water cryo-EM vitrification conditions Cryogen ETHANE；ethane vitrification	Resolution 12.00 Å
1WTH Crystal structure of gp5-S351L mutant and gp27 complex Deposited 2004-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–575（575 aa）	Mutation：S351L	K POTASSIUM ION × 3 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；279 K；PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.80 Å R-free 0.281
2Z6B Crystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III) protoporphyrin Deposited 2007-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–575（575 aa）	Mutation：N7C, S351L	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；285 K；PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.11 Å R-free 0.315
3A1M A fusion protein of a beta helix region of gene product 5 and the foldon region of bacteriophage T4 Deposited 2009-04-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 490–575（86 aa） Chain B 490–575（86 aa） Chain C 490–575（86 aa） Chain D 490–575（86 aa） Chain E 490–575（86 aa） Chain F 490–575（86 aa）	Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L	K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.268
4JIV VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5 Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain B 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain C 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575	Mutation：T566H, D568V, R571A, D573N, I574L, G575N Mutation：T566H, D568V, R571A, D573N, I574L, G575N Mutation：T566H, D568V, R571A, D573N, I574L, G575N	MG MAGNESIUM ION × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-15% PEG 2000, 100mM NaAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.208
4JIW c1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5 Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain B 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain C 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575	Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100-150mM CaCl2, 13-15% PEG 3350, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.243
4JIW c1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5 Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain F 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain G 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575	Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100-150mM CaCl2, 13-15% PEG 3350, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.243
4JIW c1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5 Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain J 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain K 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575	Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N	MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100-150mM CaCl2, 13-15% PEG 3350, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.243
4JIW c1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5 Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain N 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575 Chain O 484–575（92 aa） Fragment：gp5G484, UNP RESIDUES 484-575	Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N Mutation：T566D, D568K, S570A, R571K, D573N, I574L, G575N	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100-150mM CaCl2, 13-15% PEG 3350, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.243
4JJ2 High resolution structure of a C-terminal fragment of the T4 phage gp5 beta-helix Deposited 2013-03-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 483–575（93 aa） Fragment：UNP residues 483-575 Chain B 483–575（93 aa） Fragment：UNP residues 483-575 Chain C 483–575（93 aa） Fragment：UNP residues 483-575	Not recorded	MG MAGNESIUM ION × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.03-0.05M CaCl2, 0.1M NaAc pH 5.2, 11-15% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.28 Å R-free 0.178
4KU0 Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-helix fragment Deposited 2013-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 484–575（92 aa） Fragment：residues 484-575 Chain B 484–575（92 aa） Fragment：residues 484-575 Chain C 484–575（92 aa） Fragment：residues 484-575	Not recorded	MG MAGNESIUM ION × 1 ELA Elaidic acid × 1 EDO 1,2-ETHANEDIOL × 4 STE STEARIC ACID × 1 PLM PALMITIC ACID × 1 FE FE (III) ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；23-25% PEG 3350, 100mM Tris pH=8.5, 40-100mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.15 Å R-free 0.171
4OSD Dimer of a C-terminal fragment of phage T4 gp5 beta-helix Deposited 2014-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain B 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain C 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain D 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain E 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain F 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575	Not recorded	ELA Elaidic acid × 3 MG MAGNESIUM ION × 2 STE STEARIC ACID × 2 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22% PEG 4000, 200mM Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.96 Å R-free 0.279
4OSD Dimer of a C-terminal fragment of phage T4 gp5 beta-helix Deposited 2014-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain H 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain I 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain J 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain K 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain L 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575	Not recorded	ELA Elaidic acid × 2 MG MAGNESIUM ION × 2 STE STEARIC ACID × 2 PLM PALMITIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22% PEG 4000, 200mM Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.96 Å R-free 0.279
4OSD Dimer of a C-terminal fragment of phage T4 gp5 beta-helix Deposited 2014-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain M 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain N 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain O 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain P 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain Q 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575 Chain R 484–575（92 aa） Fragment：C-terminal fragment, UNP RESIDUES 484-575	Not recorded	ELA Elaidic acid × 2 MG MAGNESIUM ION × 2 STE STEARIC ACID × 2 PLM PALMITIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22% PEG 4000, 200mM Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.96 Å R-free 0.279
5IV5 Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex Deposited 2016-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 145 PDB declaration: 145-meric	Chain YA 1–575（575 aa） Chain YB 1–575（575 aa） Chain YC 1–575（575 aa）	Not recorded	ZN ZINC ION × 6 FE FE (III) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Applied 3.5 ul of sample and blotting 3 seconds before plunging	Resolution 4.11 Å
6P1Z Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain Deposited 2019-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 484–575（92 aa） Chain B 484–575（92 aa） Chain C 484–575（92 aa）	Not recorded	MG MAGNESIUM ION × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；47.5-50 % PEG5500 MME 100 mM Glycine pH 10 25-100 mM KBr	Resolution 2.10 Å R-free 0.251
6P1Z Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain Deposited 2019-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 484–575（92 aa） Chain F 484–575（92 aa） Chain G 484–575（92 aa）	Not recorded	MG MAGNESIUM ION × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；47.5-50 % PEG5500 MME 100 mM Glycine pH 10 25-100 mM KBr	Resolution 2.10 Å R-free 0.251
6P20 Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164 Deposited 2019-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 484–559（76 aa） Chain B 484–559（76 aa） Chain C 484–559（76 aa）	Not recorded	MG MAGNESIUM ION × 3 STE STEARIC ACID × 1 ELA Elaidic acid × 1 EDO 1,2-ETHANEDIOL × 1 PLM PALMITIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20-30% PEG 3350 100 mM MES ph 6.5 200-350 mM Mg(NO3)2	Resolution 1.75 Å R-free 0.191
6P2A Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment Deposited 2019-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 484–559（76 aa） Chain B 484–559（76 aa） Chain C 484–559（76 aa）	Not recorded	FE2 FE (II) ION × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350 18-20% 100 mM Ammonium citrate	Resolution 1.90 Å R-free 0.158
6P2A Chimera of bacteriophage OBP gp146 central spike protein and a T4 gp5 beta-helix fragment Deposited 2019-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 484–559（76 aa） Chain E 484–559（76 aa） Chain F 484–559（76 aa）	Not recorded	FE2 FE (II) ION × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350 18-20% 100 mM Ammonium citrate	Resolution 1.90 Å R-free 0.158
6XC0 Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form Deposited 2020-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 174–342（169 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SIN SUCCINIC ACID × 1 CL CHLORIDE ION × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.78 Å R-free 0.198
6XC0 Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form Deposited 2020-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 174–342（169 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.78 Å R-free 0.198
6XC1 Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form Deposited 2020-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 174–342（169 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 IPA ISOPROPYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.92 Å R-free 0.215
7CN7 T4 phage spackle protein gp61.3 complex with lysozyme domain of gp5 tail lysozyme Deposited 2020-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 162–342（181 aa）	Not recorded	1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 1 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；PEG550MME, MES, KSCN	Resolution 1.15 Å R-free 0.121

17 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BP5_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–86； UniProt 484–565 Author chain B； PDBConstruct 5–86； UniProt 484–565 Author chain C； PDBConstruct 5–86； UniProt 484–565

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

UniProt Q7N647

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 523–533 Chain B； UniProt 523–533 Chain C； UniProt 523–533	Not recorded	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN × 1 （Q7N648） MG MAGNESIUM ION × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0	Resolution 2.29 Å R-free 0.222

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 6P22	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9QGM Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state Deposited 2025-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain 8A 1–533（533 aa） Chain 8B 1–533（533 aa） Chain 8C 1–533（533 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7N647_PHOLL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 87–97； UniProt 523–533 Author chain B； PDBConstruct 87–97； UniProt 523–533 Author chain C； PDBConstruct 87–97； UniProt 523–533

PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

UniProt Q7N648

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–138	Not recorded	CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC × 3 （P16009,Q7N647） MG MAGNESIUM ION × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0	Resolution 2.29 Å R-free 0.222

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	Q7N648_PHOLL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–138； UniProt 1–138

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	6p22
Deposition date deposition_date	2019-05-20
Structure title title	Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
Keywords keywords	;PVC, Photorhabdus laumondii, membrane piercing, central spike, cell puncturing device, PAAR-repeat motif, beta helix, T4 gp5, contractile injection system, viral protein, Pvc8, Pvc10, hydrolase ;; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.93 Å
Radius of gyration Rg (electron density) rg_electron	30.78 Å
Forward intensity I(0) i0	33308800.00
Molecular weight molecular_weight	44774.0 kDa
Excluded volume excluded_volume	56007 Å³
Envelope volume envelope_volume	67573 Å³
Hydration-shell volume shell_volume	21925 Å³
Envelope diameter envelope_diameter	118.8 Å
Shell Rg shell_rg	31.80 Å
Envelope Rg envelope_rg	31.79 Å
Shape Rg shape_rg	30.77 Å
Total Rg total_rg	30.90 Å
Total atoms total_atoms	6301
Residues n_residues	419
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	115.0 Å
Rg (real space) rg_real	30.70 Å
Rg uncertainty (real space) rg_real_error	1.37 Å
I(0) (real space) i0_real	3.3310e+07
I(0) uncertainty (real space) i0_real_error	5.0330e+05
Rg (reciprocal space) rg_reciprocal	30.37 Å
I(0) (reciprocal space) i0_reciprocal	33300000.0000
Solution quality estimate total_estimate	0.6600
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.855
Kurtosis Kurtosis kurtosis	0.205
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6283000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.200; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.098; Smooth: 0.877

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
Molecular weight formula_weight	10011.9 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6455

GSGSGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLTQ

来源 Source

来源生物 organism	Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
NCBI Class编号 ncbi_taxonomy_id	243265
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
Molecular weight formula_weight	14669.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSKQLVIDGDNLLFEPLFGNRQVTILGPATIRGSGHAKIQGKKIVIVGDEKKVQLQAQYITPSHPIPGMGIVTIAQLDANQQVNFCRTPATAIVVGQQFIARFTPTQPANNPSTGPDVTTPSMGKGRFIASQYAVSAG

来源 Source

来源生物 organism	Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
NCBI Class编号 ncbi_taxonomy_id	243265
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	STEARIC ACID
Molecular weight formula_weight	284.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	Elaidic acid
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

▶

8. Citations (3)

▶

Unit-cell length a length_a	34.305 Å
Unit-cell length b length_b	56.963 Å
Unit-cell length c length_c	222.994 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	2.291 Å
Low-resolution limit resolution_low	45.213 Å
R factor r_factor	0.1840
R_work r_work	0.1819
R_free r_free	0.2224

fit	/app/data/saxs_computation/p2/6p22/6p22.fit
pddf	/app/data/pr_computation/p2/6p22/6p22.pr.out
profile	/app/data/saxs_computation/p2/6p22/6p22.dat

Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC

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

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

PAAR-REPEAT CENTRAL SPIKE TIP 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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)