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- PDB-1ogz: Crystal Structure Of 5-3-Ketosteroid Isomerase Mutants P39A Compl... -

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Basic information

Entry
Database: PDB / ID: 1ogz
TitleCrystal Structure Of 5-3-Ketosteroid Isomerase Mutants P39A Complexed With Equilenin From Pseudomonas Testosteroni
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / KETOSTEROID
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 / 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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesCOMAMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNam, G.H. / Cha, S.-S. / Yun, Y.S. / Oh, Y.H. / Hong, B.H. / Lee, H.-S. / Choi, K.Y.
CitationJournal: Biochem.J. / Year: 2003
Title: The Conserved Cis-Pro39 Residue Plays a Crucial Role in the Proper Positioning of the Catalytic Base Asp38 in Ketosteroid Isomerase from Comamonas Testosteroni.
Authors: Nam, G.H. / Cha, S. / Yun, Y.S. / Oh, Y.H. / Hong, B.H. / Lee, H. / Choi, K.Y.
History
DepositionMay 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2003Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6642
Polymers13,3981
Non-polymers2661
Water1,67593
1
A: STEROID DELTA-ISOMERASE
hetero molecules

A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3294
Polymers26,7962
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)60.733, 60.733, 142.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 13398.118 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: D-EQUILENIN BINDING AT HYDROPHOBIC POCKET. / Source: (gene. exp.) COMAMONAS TESTOSTERONI (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION PRO39ALA CATALYTIC ACTIVITY: A 3-OXO-DELTA(5)-STEROID = A 3-OXO-DELTA(4)- STEROID.

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 21.9-22.1 K / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mg/mlDMSO1drop
210 mg/ml1dropKSI
32.0 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 2
DetectorType: MACSCIENCE DIP2030 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 10000 / % possible obs: 98 % / Redundancy: 2 %
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 95.3 % / Rmerge(I) obs: 0.065

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.309 --
Rwork0.235 --
obs0.235 10000 70 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 20 93 1057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.1
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_deg1.7
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
Refinement
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.083
X-RAY DIFFRACTIONc_angle_deg3.172

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