6jjo

Crystal structure of the DegP dodecamer with a modulator

Method: X-RAY DIFFRACTION D_max: 169.9 Å Quality: REASONABLE

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

Periplasmic serine endoprotease DegP

Escherichia coli K-12

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric（36） Consistent with protein copy count	Chain A； UniProt 27–474 Chain B； UniProt 27–474 Chain C； UniProt 27–474 Chain D； UniProt 27–474 Chain E； UniProt 27–474 Chain F； UniProt 27–474	Mutation：S210A	TMB-CYRKL modulator × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350 and 0.1 M tacsimate pH 3.5	Resolution 4.16 Å R-free 0.278

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 6JJO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KY9 Crystal Structure of DegP (HtrA) Deposited 2002-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 27–474（448 aa）	Mutation：S210A 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, SITTING DROP；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.80 Å R-free 0.275
1KY9 Crystal Structure of DegP (HtrA) Deposited 2002-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 27–474（448 aa）	Mutation：S210A 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, SITTING DROP；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.80 Å R-free 0.275
2ZLE Cryo-EM structure of DegP12/OMP Deposited 2008-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 27–474（448 aa） Chain B 27–474（448 aa） Chain C 27–474（448 aa） Chain E 27–474（448 aa） Chain F 27–474（448 aa） Chain G 27–474（448 aa） Chain H 27–474（448 aa） Chain I 27–474（448 aa） Chain J 27–474（448 aa） Chain K 27–474（448 aa） Chain L 27–474（448 aa） Chain M 27–474（448 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity	Resolution 28.00 Å
3CS0 Crystal structure of DegP24 Deposited 2008-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain A 27–474（448 aa）	Mutation：S210A 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；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, vapor diffusion, temperature 292K	Resolution 3.00 Å R-free 0.274
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 27–474（448 aa）	Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.10 Å R-free 0.309
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 27–474（448 aa）	Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.10 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	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 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.00 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	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 B 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.00 Å R-free 0.309
3MH6 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 27–474（448 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.60 Å R-free 0.309
3MH7 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 27–474（448 aa）	Mutation：S210A 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；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 292K	Resolution 2.96 Å R-free 0.249
3OTP Crystal structure of the DegP dodecamer with a model substrate Deposited 2010-09-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 27–474（448 aa） Fragment：UNP residues 27-474 Chain B 27–474（448 aa） Fragment：UNP residues 27-474 Chain C 27–474（448 aa） Fragment：UNP residues 27-474 Chain D 27–474（448 aa） Fragment：UNP residues 27-474 Chain E 27–474（448 aa） Fragment：UNP residues 27-474 Chain F 27–474（448 aa） Fragment：UNP residues 27-474	Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；291 K；65 mM citric acid, 35 mM Bis-Tris propane, 8% PEG3350, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K	Resolution 3.76 Å R-free 0.251
3OU0 re-refined 3CS0 Deposited 2010-09-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 27–474（448 aa） Fragment：DegP, UNP residues 27-474	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.229
4A8D DegP dodecamer with bound OMP Deposited 2011-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 27–474（448 aa） Fragment：DEGP Chain B 27–474（448 aa） Fragment：DEGP Chain C 27–474（448 aa） Fragment：DEGP Chain D 27–474（448 aa） Fragment：DEGP Chain E 27–474（448 aa） Fragment：DEGP Chain F 27–474（448 aa） Fragment：DEGP Chain G 27–474（448 aa） Fragment：DEGP Chain H 27–474（448 aa） Fragment：DEGP Chain I 27–474（448 aa） Fragment：DEGP Chain J 27–474（448 aa） Fragment：DEGP Chain K 27–474（448 aa） Fragment：DEGP Chain L 27–474（448 aa） Fragment：DEGP	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 300MM NACL, 50MM HEPES- NAOH；pH 8；300MM NACL, 50MM HEPES- NAOH cryo-EM vitrification conditions Cryogen ETHANE；EMBEDDED IN VITREOUS ICE USING C-FLAT HOLEY CARBON GRIDS AND A VITROBOT AT 20C.	Resolution 28.00 Å
6JJK Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 35–474（440 aa） Chain B 35–474（440 aa） Chain C 35–474（440 aa） Chain D 35–474（440 aa） Chain E 35–474（440 aa） Chain F 35–474（440 aa）	Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；10% PEG3350 and 0.1 M tacsimate pH 3.4	Resolution 3.60 Å R-free 0.265
6JJL Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 35–474（440 aa） Chain B 35–474（440 aa） Chain C 35–474（440 aa） Chain D 35–474（440 aa） Chain E 35–474（440 aa） Chain F 35–474（440 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350, 0.1 M tacsimate pH 3.5	Resolution 4.20 Å R-free 0.326
8F0A Client-bound structure of a DegP trimer within a 12mer cage Deposited 2022-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.60 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 12.10 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 13.80 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 90 PDB declaration: 90-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474) Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 14.10 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385) Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.70 Å

18 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEGP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–469； UniProt 27–474 Author chain B； PDBConstruct 22–469； UniProt 27–474 Author chain C； PDBConstruct 22–469； UniProt 27–474 Author chain D； PDBConstruct 22–469； UniProt 27–474 Author chain E； PDBConstruct 22–469； UniProt 27–474 Author chain F； PDBConstruct 22–469； UniProt 27–474

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	6jjo
Deposition date deposition_date	2019-02-26
Structure title title	Crystal structure of the DegP dodecamer with a modulator
Keywords keywords	Protease, HYDROLASE; HYDROLASE
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	52.12 Å
Radius of gyration Rg (electron density) rg_electron	51.77 Å
Forward intensity I(0) i0	863931000.00
Molecular weight molecular_weight	241240.0 kDa
Excluded volume excluded_volume	301320 Å³
Envelope volume envelope_volume	510130 Å³
Hydration-shell volume shell_volume	81279 Å³
Envelope diameter envelope_diameter	162.5 Å
Shell Rg shell_rg	58.73 Å
Envelope Rg envelope_rg	48.95 Å
Shape Rg shape_rg	51.74 Å
Total Rg total_rg	52.10 Å
Total atoms total_atoms	16906
Residues n_residues	2370
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	169.9 Å
Rg (real space) rg_real	51.95 Å
Rg uncertainty (real space) rg_real_error	1.58 Å
I(0) (real space) i0_real	8.6390e+08
I(0) uncertainty (real space) i0_real_error	1.7100e+07
Rg (reciprocal space) rg_reciprocal	52.24 Å
I(0) (reciprocal space) i0_reciprocal	864300000.0000
Solution quality estimate total_estimate	0.6059
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	79.3 Å
Skewness Skewness skewness	0.010
Kurtosis Kurtosis kurtosis	-0.790
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58500000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Periplasmic serine endoprotease DegP
Molecular weight formula_weight	49155.5 kDa
EC 编号 ec_number	3.4.21.107
Mutation mutation	S210A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16906

MGSSHHHHHHSSGLVPRGSHMAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TMB-CYRKL modulator
Molecular weight formula_weight	683.9 kDa
Source method src_method	syn
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,M,H,N,I,O,J,P,K,Q,L,R

CYRKL

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8. Citations (1)

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Unit-cell length a length_a	217.148 Å
Unit-cell length b length_b	123.518 Å
Unit-cell length c length_c	140.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	4.157 Å
Low-resolution limit resolution_low	35.610 Å
R factor r_factor	0.2191
R_work r_work	0.2158
R_free r_free	0.2780

fit	/app/data/saxs_computation/jj/6jjo/6jjo.fit
pddf	/app/data/pr_computation/jj/6jjo/6jjo.pr.out
profile	/app/data/saxs_computation/jj/6jjo/6jjo.dat

Crystal structure of the DegP dodecamer with a modulator

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

Periplasmic serine endoprotease DegP

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 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)