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Yorodumi- PDB-1buq: SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1buq | ||||||
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Title | SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19-NORTESTOSTERONE-HEMISUCCINATE | ||||||
Components | PROTEIN (3-KETOSTEROID ISOMERASE-19-NORTESTOSTERONE-HEMISUCCINATE) | ||||||
Keywords | ISOMERASE / KETOSTEROID ISOMERASE-19NTHS / ENZYME-SUBSTRATE COMPLEX / ENZYMES | ||||||
Function / homology | Function and homology information steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, REFINEMENT CALCULATIONS | ||||||
Authors | Massiah, M.A. / Abeygunawardana, C. / Gittis, A.G. / Mildvan, A.S. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Solution structure of Delta 5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone hemisuccinate. Authors: Massiah, M.A. / Abeygunawardana, C. / Gittis, A.G. / Mildvan, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1buq.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1buq.ent.gz | 942.7 KB | Display | PDB format |
PDBx/mmJSON format | 1buq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1buq ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1buq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13380.102 Da / Num. of mol.: 2 / Mutation: Y55F,Y88F Source method: isolated from a genetically manipulated source Details: KSI COMPLEXED WITH 19-NORTESTOSTERONE-HEMISUCCINATE, A SUBSTRATE ANALOG. Source: (gene. exp.) Comamonas testosteroni (bacteria) / Description: PET-25B+GENE / Plasmid: PET-25B / Cell line (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P00947, steroid Delta-isomerase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE OF THE 3-KETOSTEROID ISOMERASE 19-NORTESTOSTERONE HEMISUCCINATE ( 19-NTHS) COMPLEX WAS DETERMINED FROM BOTH 2D NOESY, 3D NOESY AND TRIPLE RESONANCE NMR SPECTRA ON AN UNLABELED ...Text: THE STRUCTURE OF THE 3-KETOSTEROID ISOMERASE 19-NORTESTOSTERONE HEMISUCCINATE ( 19-NTHS) COMPLEX WAS DETERMINED FROM BOTH 2D NOESY, 3D NOESY AND TRIPLE RESONANCE NMR SPECTRA ON AN UNLABELED SAMPLE (2D NOESY), 15N-LABELED, 13C-, 15N-UNIFORMLY LABELED, AND/OR 13C-,15N/15N-HETEROLABELED ISOMERASE WITH 1.1 MM 19-NTHS. 3D NOESY AND TRIPLE RESONACE SPECTRA ON THE 15N-UNIFORMLY LABELED AND 13C-,15N-UNIFORMLY SAMPLES WERE USED FOR 1H, 15N,13C ASSIGNMENTS AS WELL AS STRUCTURAL INFORMATION FOR EACH SUBUNIT. THE 1H-13C-FILTERED NOESY-HSQC OF A 13C, 15N/15N-HETEROLABELED SAMPLE PROVIDED CRITICAL NOES BETWEEN THE IDENTICAL MONOMERS OF THE HOMODIMER WHICH LED TO THE SOLUTION STRUCTURE OF KSI COMPLEXED TO 19-NTHS. |
-Sample preparation
Sample conditions | Ionic strength: 30 mM / pH: 7.2 / Pressure: 1 atm / Temperature: 310 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING, REFINEMENT CALCULATIONS Software ordinal: 1 Details: DURING THE REFINEMENT, THE NON-BONDED INTERACTIONS WERE MODELED ONLY BY A QUADRATIC REPULSIVE ENERGY TERM, WHILE THE ATTRACTIVE COMPONENT OF THE LENNARD- JONES POTENTIAL AND THE ...Details: DURING THE REFINEMENT, THE NON-BONDED INTERACTIONS WERE MODELED ONLY BY A QUADRATIC REPULSIVE ENERGY TERM, WHILE THE ATTRACTIVE COMPONENT OF THE LENNARD- JONES POTENTIAL AND THE ELECTROSTATIC ENERGY WERE TURNED OFF. AT THE FINAL STAGES OF REFINEMENT, A SQUARE-WELL POTENTIAL ENERGY FUNCTION WAS USED FOR THE NOE AND THE DIHEDRAL ANGLE RESTRANTS WITH A FORCE OF 500 KCAL MOL-1 ANG-2 AND 200 KCAL MOL-1 RAD-2, RESPECTIVELY. OF THE 120 EMBEDDED SUBSTRUCTURES, 60 CONVERGED TO ACCEPTABLE STRUCTURES WITH NOE VIOLATION EQUAL OR LESS THAN 0.5ANG. OF THESE, 15 BEST STRUCTURES WITH NOE VIOLATIONS EQUAL OR LESS THAN 0.35 ANG AND DIHEDRAL VIOLATION < 5 DEG WERE SELECTED. MODEL 1 (STRUCTURE 1) OF THE 15 STRUCTURES OF THE KSI-19NTHS COMPLEX IS THE LOWEST ENERGY STRUCTURE. | ||||||||||||
NMR ensemble | Conformer selection criteria: NOE VIOLATION =< 0.35A AND DIHEDRAL VIOLATION < 5 DEG. Conformers calculated total number: 120 / Conformers submitted total number: 15 |