3m8c

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound

Method: X-RAY DIFFRACTION D_max: 100.7 Å Quality: GOOD

▼

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

Steroid Delta-isomerase

Comamonas testosteroni

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 1–125 Chain B； UniProt 1–125	Mutation：D99N	GOL GLYCEROL × 2 SO4 SULFATE ION × 7 EQU EQUILENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：sitting drop；pH 7.2；298 K；1.4 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, sitting drop, temperature 298K	Resolution 2.10 Å R-free 0.222
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–125 Chain D； UniProt 1–125	Mutation：D99N	SO4 SULFATE ION × 6 EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：sitting drop；pH 7.2；298 K；1.4 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, sitting drop, temperature 298K	Resolution 2.10 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 3M8C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUQ SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19-NORTESTOSTERONE-HEMISUCCINATE Deposited 1998-09-04	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：Y55F,Y88F Mutation：Y55F,Y88F	NTH SUCCINIC ACID MONO-(13-METHYL-3-OXO-2,3,6,7,8,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHREN-17-YL) ESTER × 2	SOLUTION NMR NMR measurement conditions pH 7.2；310 K；Ionic strength (raw mmCIF value) 30 mM；Pressure 1	Resolution not provided
1ISK 3-OXO-DELTA5-STEROID ISOMERASE, NMR, 20 STRUCTURES Deposited 1997-03-12	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K	Resolution not provided
1OCV the F116W mutant structure of ketosteroid isomerase from Comamonas testosteroni Deposited 2003-02-11	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.00 Å R-free 0.282
1OCV the F116W mutant structure of ketosteroid isomerase from Comamonas testosteroni Deposited 2003-02-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.00 Å R-free 0.282
1OGZ Crystal Structure Of 5-3-Ketosteroid Isomerase Mutants P39A Complexed With Equilenin From Pseudomonas Testosteroni Deposited 2003-05-20	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 1–125（125 aa）	Mutation：YES	EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.30 Å R-free 0.309
1OHP CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH 5ALPHA-ESTRAN-3,17-DIONE Deposited 2003-05-29	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：YES Mutation：YES	ESR 5-ALPHA-ESTRAN-3,17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4K 24%, 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6	Resolution 1.53 Å R-free 0.229
1OHP CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH 5ALPHA-ESTRAN-3,17-DIONE Deposited 2003-05-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：YES Mutation：YES	ESR 5-ALPHA-ESTRAN-3,17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4K 24%, 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6	Resolution 1.53 Å R-free 0.229
1OHS CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT Y14F/D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH ANDROSTANEDIONE Deposited 2003-05-30	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：YES Mutation：YES	5SD 5ALPHA-ANDROSTAN-3,17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4K 20% 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6	Resolution 1.70 Å R-free 0.249
1OHS CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT Y14F/D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH ANDROSTANEDIONE Deposited 2003-05-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：YES Mutation：YES	5SD 5ALPHA-ANDROSTAN-3,17-DIONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4K 20% 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6	Resolution 1.70 Å R-free 0.249
1QJG Crystal structure of delta5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin Deposited 1999-06-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：YES Mutation：YES	EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4000 25%, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.271
1QJG Crystal structure of delta5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin Deposited 1999-06-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：YES Mutation：YES	EQU EQUILENIN × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4000 25%, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.271
1QJG Crystal structure of delta5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin Deposited 1999-06-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–125（125 aa） Chain F 1–125（125 aa）	Mutation：YES Mutation：YES	EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PEG 4000 25%, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.271
3MHE Crystal Structure of Ketosteroid Isomerase P39A from Pseudomonas Testosteroni (tKSI) Deposited 2010-04-07	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：P39A Mutation：P39A	SO4 SULFATE ION × 7 POL N-PROPANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；2.0 M ammonium sulfate, 5% propanol, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.72 Å R-free 0.233
3MKI Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI) Deposited 2010-04-14	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D38E, D99N Mutation：D38E, D99N	SO4 SULFATE ION × 11 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；1.2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.213
3MKI Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI) Deposited 2010-04-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：D38E, D99N Mutation：D38E, D99N	SO4 SULFATE ION × 10 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；1.2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.213
3MKI Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI) Deposited 2010-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–125（125 aa） Chain B 1–125（125 aa） Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：D38E, D99N Mutation：D38E, D99N Mutation：D38E, D99N Mutation：D38E, D99N	SO4 SULFATE ION × 42 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；1.2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.213
3MYT Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) Deposited 2010-05-11	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 1–125（125 aa） Chain C 1–125（125 aa）	Mutation：D38HD99N Mutation：D38HD99N	SO4 SULFATE ION × 6 EQU EQUILENIN × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 7.2；298 K；1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K	Resolution 1.96 Å R-free 0.282
3MYT Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) Deposited 2010-05-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：D38HD99N Mutation：D38HD99N	SO4 SULFATE ION × 9 EQU EQUILENIN × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 7.2；298 K；1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K	Resolution 1.96 Å R-free 0.282
3MYT Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) Deposited 2010-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–125（125 aa） Chain B 1–125（125 aa） Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：D38HD99N Mutation：D38HD99N Mutation：D38HD99N Mutation：D38HD99N	SO4 SULFATE ION × 30 EQU EQUILENIN × 6 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 7.2；298 K；1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K	Resolution 1.96 Å R-free 0.282
3MYT Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) Deposited 2010-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–125（125 aa） Chain B 1–125（125 aa） Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：D38HD99N Mutation：D38HD99N Mutation：D38HD99N Mutation：D38HD99N	SO4 SULFATE ION × 15 EQU EQUILENIN × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 7.2；298 K；1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K	Resolution 1.96 Å R-free 0.282
3NBR Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound Deposited 2010-06-03	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 1–125（125 aa）	Mutation：D38NP39GD99N	SO4 SULFATE ION × 6 ASD 4-ANDROSTENE-3-17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K	Resolution 1.73 Å R-free 0.265
3NHX Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound Deposited 2010-06-14	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 1–125（125 aa）	Mutation：D99N	ASD 4-ANDROSTENE-3-17-DIONE × 2 SO4 SULFATE ION × 20	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；298 K；2 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.59 Å R-free 0.219
3NM2 Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI) Deposited 2010-06-21	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 1–125（125 aa）	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2.0 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.89 Å R-free 0.254
3NUV Crystal structure of ketosteroid isomerase D38ND99N from Pseudomonas testosteroni (tKSI) with 4-Androstene-3,17-dione Bound Deposited 2010-07-07	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D38N, D99N Mutation：D38N, D99N	ASD 4-ANDROSTENE-3-17-DIONE × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；298 K；1.8 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.76 Å R-free 0.198
3NUV Crystal structure of ketosteroid isomerase D38ND99N from Pseudomonas testosteroni (tKSI) with 4-Androstene-3,17-dione Bound Deposited 2010-07-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D38N, D99N Mutation：D38N, D99N	ASD 4-ANDROSTENE-3-17-DIONE × 4 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；298 K；1.8 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.76 Å R-free 0.198
3NXJ Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) Deposited 2010-07-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D99N Mutation：D99N	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；2.0 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.97 Å R-free 0.314
3NXJ Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) Deposited 2010-07-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D99N Mutation：D99N	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；2.0 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.97 Å R-free 0.314
3OV4 Crystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseudomonas Testosteroni (tKSI) bound to Equilenin Deposited 2010-09-15	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：P39G V40G S42G Mutation：P39G V40G S42G	SO4 SULFATE ION × 7 EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；10mg/ml protein, 1.8 M ammonium sulfate, 40mM potassium phosphate , 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.83 Å R-free 0.228
3OV4 Crystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseudomonas Testosteroni (tKSI) bound to Equilenin Deposited 2010-09-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：P39G V40G S42G Mutation：P39G V40G S42G	SO4 SULFATE ION × 6 EQU EQUILENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；10mg/ml protein, 1.8 M ammonium sulfate, 40mM potassium phosphate , 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.83 Å R-free 0.228
3T8U Crystal structure of ketosteroid isomerase Y14AY55FD99A from Pseudomonas testosteroni Deposited 2011-08-01	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：Y14A, Y55F, D99A Mutation：Y14A, Y55F, D99A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；2.0 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.300
3T8U Crystal structure of ketosteroid isomerase Y14AY55FD99A from Pseudomonas testosteroni Deposited 2011-08-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：Y14A, Y55F, D99A Mutation：Y14A, Y55F, D99A	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；2.0 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.300
3UNL Crystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni Deposited 2011-11-15	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：F54G Mutation：F54G	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；1.4 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.52 Å R-free 0.268
3UNL Crystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni Deposited 2011-11-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain D 1–125（125 aa）	Mutation：F54G Mutation：F54G	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；1.4 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.52 Å R-free 0.268
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	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 1–125（125 aa） Chain B 1–125（125 aa）	Mutation：D38E Mutation：D38E	GOL GLYCEROL × 1 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa） Chain J 1–125（125 aa）	Mutation：D38E Mutation：D38E	GOL GLYCEROL × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–125（125 aa） Chain I 1–125（125 aa）	Mutation：D38E Mutation：D38E	GOL GLYCEROL × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–125（125 aa） Chain G 1–125（125 aa）	Mutation：D38E Mutation：D38E	GOL GLYCEROL × 1 SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain F 1–125（125 aa） Chain K 1–125（125 aa）	Mutation：D38E Mutation：D38E	GOL GLYCEROL × 1 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
4L7K Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) Deposited 2013-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 1–125（125 aa） Chain O 1–125（125 aa）	Mutation：D38E Mutation：D38E	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.354
5DRE Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI) Deposited 2015-09-15	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 1–125（125 aa）	Mutation：D38G, P39G, D99N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Potassium Phosphate 40 mM, Ammonium Sulfate 0.6 M	Resolution 2.15 Å R-free 0.268
5UGI Crystal Structure of Ketosteroid Isomerase D38GF54A mutant from Pseudomonas Testosteroni (tKSI) bound to Equilenin Deposited 2017-01-08	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 1–125（125 aa）	Mutation：D38G, F54A	EQU EQUILENIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40 mM Potassium Phosphate, 1.0 M Ammonium Sulfate, 0.25 M Trimethyl acetate	Resolution 1.80 Å R-free 0.227
8CHO CRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE FROM PSEUDOMONAS TESTOSTERONI Deposited 1998-01-06	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 1–125（125 aa）	Not recorded	P4C O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.271

22 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SDIS_COMTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125 Author chain C； PDBConstruct 1–125； UniProt 1–125 Author chain D； PDBConstruct 1–125； UniProt 1–125

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3m8c
Deposition date deposition_date	2010-03-17
Structure title title	Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound
Keywords keywords	Isomerase, Lipid metabolism, Steroid metabolism; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.75 Å
Radius of gyration Rg (electron density) rg_electron	30.30 Å
Forward intensity I(0) i0	52346200.00
Molecular weight molecular_weight	55456.0 kDa
Excluded volume excluded_volume	68737 Å³
Envelope volume envelope_volume	87587 Å³
Hydration-shell volume shell_volume	25350 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	35.52 Å
Envelope Rg envelope_rg	30.49 Å
Shape Rg shape_rg	30.28 Å
Total Rg total_rg	30.84 Å
Total atoms total_atoms	3893
Residues n_residues	496
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	100.7 Å
Rg (real space) rg_real	30.97 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	5.2350e+07
I(0) uncertainty (real space) i0_real_error	8.5930e+05
Rg (reciprocal space) rg_reciprocal	30.88 Å
I(0) (reciprocal space) i0_reciprocal	52340000.0000
Solution quality estimate total_estimate	0.7648
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.697
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14620000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.709; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Steroid Delta-isomerase
Molecular weight formula_weight	13411.1 kDa
EC 编号 ec_number	5.3.3.1
Mutation mutation	D99N
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4703

MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPINHFRFNGAGKVVSMRALFGEKNIHAGA

来源 Source

来源生物 organism	Comamonas testosteroni
通用名 common_name	Pseudomonas testosteroni
NCBI Class编号 ncbi_taxonomy_id	285
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	EQUILENIN
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	466

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3m8ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d3m8cb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d3m8cc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d3m8cd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.3 — Ketosteroid isomerase-like

CATH v4.4 (4 domains)

Domain ID domain_id	3m8cA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3m8cB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3m8cC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3m8cD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	64.312 Å
Unit-cell length b length_b	64.312 Å
Unit-cell length c length_c	506.174 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	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	84.360 Å
R factor r_factor	0.1690
R_work r_work	0.1660
R_free r_free	0.2220

fit	/app/data/saxs_computation/m8/3m8c/3m8c.fit
pddf	/app/data/pr_computation/m8/3m8c/3m8c.pr.out
profile	/app/data/saxs_computation/m8/3m8c/3m8c.dat