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- PDB-1buq: SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1buq
TitleSOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19-NORTESTOSTERONE-HEMISUCCINATE
ComponentsPROTEIN (3-KETOSTEROID ISOMERASE-19-NORTESTOSTERONE-HEMISUCCINATE)
KeywordsISOMERASE / 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
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-NTH / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, REFINEMENT CALCULATIONS
AuthorsMassiah, M.A. / Abeygunawardana, C. / Gittis, A.G. / Mildvan, A.S.
CitationJournal: 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
DepositionSep 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (3-KETOSTEROID ISOMERASE-19-NORTESTOSTERONE-HEMISUCCINATE)
B: PROTEIN (3-KETOSTEROID ISOMERASE-19-NORTESTOSTERONE-HEMISUCCINATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5094
Polymers26,7602
Non-polymers7492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 120NOE VIOLATION =< 0.35A AND DIHEDRAL VIOLATION < 5 DEG.
RepresentativeModel #1

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Components

#1: Protein PROTEIN (3-KETOSTEROID ISOMERASE-19-NORTESTOSTERONE-HEMISUCCINATE) / KSI


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 ChemComp-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


Mass: 374.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30O5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D 1H-15N HSQC
1412D 1H-13C CT-HSQC
1513D 1H-13C-FILTERED NOESY-HSQC
1613D 1H-15N TOCSY-HSQC
1713D 1H-13C-NOESY-HSQC
1813D 1H-15N HMQC-NOESY-HSQC
1913D (H)CCH-TOCSY
11013D 1H-13C HMQC-NOESY-HSQC
11113D HNCO
11213D HN(CA)CB
NMR detailsText: 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.

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Sample preparation

Sample conditionsIonic strength: 30 mM / pH: 7.2 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
X-PLOR3.8structure solution
RefinementMethod: 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 ensembleConformer selection criteria: NOE VIOLATION =< 0.35A AND DIHEDRAL VIOLATION < 5 DEG.
Conformers calculated total number: 120 / Conformers submitted total number: 15

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