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- PDB-1ohs: CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT Y14F/D38N F... -

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Basic information

Entry
Database: PDB / ID: 1ohs
TitleCRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT Y14F/D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH ANDROSTANEDIONE
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / INHIBITOR / ANDROSTANEDIONE
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 domain / Nuclear transport factor 2 (NTF2) 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
5ALPHA-ANDROSTAN-3,17-DIONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.7 Å
AuthorsByun, M. / Kim, M.-S. / Oh, B.-H.
CitationJournal: To be Published
Title: Crystal Structure of 5-3-Ketosteroid Isomerase Mutant Y14F/D38N from Pseudomonas Testosteroni Complexed with Androstanedione
Authors: Byun, M. / Kim, M.-S. / Oh, B.-H.
History
DepositionMay 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE
C: STEROID DELTA-ISOMERASE
D: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4947
Polymers53,6294
Non-polymers8653
Water7,548419
1
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3914
Polymers26,8142
Non-polymers5772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: STEROID DELTA-ISOMERASE
D: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1033
Polymers26,8142
Non-polymers2881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.418, 95.616, 60.698
Angle α, β, γ (deg.)90.00, 90.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
STEROID DELTA-ISOMERASE / DELTA-5-3-KETOSTEROID ISOMERASE / KETOSTEROID ISOMERASE


Mass: 13407.171 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS TESTOSTERONI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical ChemComp-5SD / 5ALPHA-ANDROSTAN-3,17-DIONE


Mass: 288.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS A-D ENGINEERED MUTATIONS TYR14PHE AND ASP38ASN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growpH: 4.6
Details: PEG 4K 20% 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorDate: Dec 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 49517 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 40
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.3 / % possible all: 90.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.7→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2354 5 %RANDOM
Rwork0.219 ---
obs0.219 47097 95.4 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 63 419 4262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.215
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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