SAXSdb — 1ny5

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

transcriptional regulator (NtrC family)

Aquifex aeolicus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–387 Chain B； UniProt 1–387	Fragment：Regulatory and Central domain	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；sodium/potasium phosphate, citric acid,imidazole,methanol,glycerol,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.257

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 1NY5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NY6 Crystal structure of sigm54 activator (AAA+ ATPase) in the active state Deposited 2003-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 122–387（266 aa） Fragment：residues 122-387 Chain B 122–387（266 aa） Fragment：residues 122-387 Chain C 122–387（266 aa） Fragment：residues 122-387 Chain D 122–387（266 aa） Fragment：residues 122-387 Chain E 122–387（266 aa） Fragment：residues 122-387 Chain F 122–387（266 aa） Fragment：residues 122-387 Chain G 122–387（266 aa） Fragment：residues 122-387	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.329
1NY6 Crystal structure of sigm54 activator (AAA+ ATPase) in the active state Deposited 2003-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 122–387（266 aa） Fragment：residues 122-387 Chain I 122–387（266 aa） Fragment：residues 122-387 Chain J 122–387（266 aa） Fragment：residues 122-387 Chain K 122–387（266 aa） Fragment：residues 122-387 Chain L 122–387（266 aa） Fragment：residues 122-387 Chain M 122–387（266 aa） Fragment：residues 122-387 Chain N 122–387（266 aa） Fragment：residues 122-387	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.329
1ZY2 Crystal structure of the phosphorylated receiver domain of the transcription regulator NtrC1 from Aquifex aeolicus Deposited 2005-06-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；310 K；PEG-3350, AMMONIUM CHLORIDE, GLYCEROL, CITRIC ACID, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 3.03 Å R-free 0.283
3M0E Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain Deposited 2010-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 122–387（266 aa） Fragment：ATP-ase domain Chain B 122–387（266 aa） Fragment：ATP-ase domain Chain C 122–387（266 aa） Fragment：ATP-ase domain Chain D 122–387（266 aa） Fragment：ATP-ase domain Chain E 122–387（266 aa） Fragment：ATP-ase domain Chain F 122–387（266 aa） Fragment：ATP-ase domain Chain G 122–387（266 aa） Fragment：ATP-ase domain	Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M SODIUM CITRATE, 0.01 M FECL3, 0-5% (V/V) JEFFAMINE M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.63 Å R-free 0.241
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: helical	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: helical	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4L4U Crystal structure of construct containing A. aeolicus NtrC1 receiver, central and DNA binding domains Deposited 2013-06-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–439（439 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.248
4L5E Crystal structure of A. aeolicus NtrC1 DNA binding domain Deposited 2013-06-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 393–438（46 aa） Fragment：unp residues 393-438	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.34 Å R-free 0.206
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	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 121–387（267 aa） Fragment：UNP residues 121-387 Chain B 121–387（267 aa） Fragment：UNP residues 121-387 Chain C 121–387（267 aa） Fragment：UNP residues 121-387 Chain D 121–387（267 aa） Fragment：UNP residues 121-387 Chain E 121–387（267 aa） Fragment：UNP residues 121-387 Chain F 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	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 121–387（267 aa） Fragment：UNP residues 121-387 Chain H 121–387（267 aa） Fragment：UNP residues 121-387 Chain I 121–387（267 aa） Fragment：UNP residues 121-387 Chain J 121–387（267 aa） Fragment：UNP residues 121-387 Chain K 121–387（267 aa） Fragment：UNP residues 121-387 Chain L 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	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 121–387（267 aa） Fragment：UNP residues 121-387 Chain N 121–387（267 aa） Fragment：UNP residues 121-387 Chain O 121–387（267 aa） Fragment：UNP residues 121-387 Chain P 121–387（267 aa） Fragment：UNP residues 121-387 Chain Q 121–387（267 aa） Fragment：UNP residues 121-387 Chain R 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain S 121–387（267 aa） Fragment：UNP residues 121-387 Chain T 121–387（267 aa） Fragment：UNP residues 121-387 Chain U 121–387（267 aa） Fragment：UNP residues 121-387 Chain V 121–387（267 aa） Fragment：UNP residues 121-387 Chain W 121–387（267 aa） Fragment：UNP residues 121-387 Chain X 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	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 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain B 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain C 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain D 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain E 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain F 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	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 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain H 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain I 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain J 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain K 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain L 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	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 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain N 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain O 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain P 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain Q 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain R 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain S 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain T 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain U 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain V 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain W 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain X 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
9MSE de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring) Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9MSF de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring) Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9MSG De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

12 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O67198_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–387； UniProt 1–387 Author chain B； PDBConstruct 1–387； UniProt 1–387

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ny5
Deposition date deposition_date	2003-02-11
Structure title title	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Keywords keywords	AAA+ ATPase, sigma54 activator, bacterial transcription, dimer, TRANSCRIPTION; TRANSCRIPTION
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	30.14 Å
Radius of gyration Rg (electron density) rg_electron	29.41 Å
Forward intensity I(0) i0	119849000.00
Molecular weight molecular_weight	89323.0 kDa
Excluded volume excluded_volume	113220 Å³
Envelope volume envelope_volume	140940 Å³
Hydration-shell volume shell_volume	39407 Å³
Envelope diameter envelope_diameter	93.8 Å
Shell Rg shell_rg	37.31 Å
Envelope Rg envelope_rg	28.97 Å
Shape Rg shape_rg	29.39 Å
Total Rg total_rg	30.24 Å
Total atoms total_atoms	6277
Residues n_residues	769
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	94.9 Å
Rg (real space) rg_real	30.04 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.1980e+08
I(0) uncertainty (real space) i0_real_error	1.9570e+06
Rg (reciprocal space) rg_reciprocal	30.08 Å
I(0) (reciprocal space) i0_reciprocal	119900000.0000
Solution quality estimate total_estimate	0.8321
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.205
Kurtosis Kurtosis kurtosis	-0.521
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39900000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	transcriptional regulator (NtrC family)
Molecular weight formula_weight	44302.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6545

MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKFIDRGELSCLVNSK

来源 Source

来源生物 organism	Aquifex aeolicus
NCBI Class编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ny5a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

Domain ID domain_id	d1ny5a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny5b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

Domain ID domain_id	d1ny5b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (6 domains)

Domain ID domain_id	1ny5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1ny5A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny5A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1ny5B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny5B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

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8. Citations (1)

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Unit-cell length a length_a	94.765 Å
Unit-cell length b length_b	94.765 Å
Unit-cell length c length_c	195.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	42.620 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2570

fit	/app/data/saxs_computation/ny/1ny5/1ny5.fit
pddf	/app/data/pr_computation/ny/1ny5/1ny5.pr.out
profile	/app/data/saxs_computation/ny/1ny5/1ny5.dat

Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state