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- PDB-1e97: Crystal structure of ketosteroid isomerase from Pseudomonas putid... -

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Basic information

Entry
Database: PDB / ID: 1.0E+97
TitleCrystal structure of ketosteroid isomerase from Pseudomonas putida ; triple mutant y16f/y32f/y57f
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / KETOSTEROID ISOMERASE / LBHB
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsHa, N.-C. / Oh, B.-H.
CitationJournal: Biochemistry / Year: 2001
Title: Peudoreversion of the Catalytic Activity of Y14F by the Additional Substitution(S) of Tyrosine with Phenylalanine in the Hydrogen Bond Network of Delta 5-3-Ketosteroid Isomerase from Pseudomonas Putida Biotype B
Authors: Choi, G. / Ha, N.-C. / Kim, M.-S. / Hong, B.-H. / Kim, D.-H. / Oh, B.-H. / Choi, K.Y.
History
DepositionOct 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2001Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)14,5011
Polymers14,5011
Non-polymers00
Water86548
1
A: STEROID DELTA-ISOMERASE

A: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)29,0012
Polymers29,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)36.330, 96.530, 74.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein STEROID DELTA-ISOMERASE / KSI


Mass: 14500.501 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION TYR16PHE, TYR32PHE, TYR57PHE

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Kim, S.W., (1997) Biochemistry, 36, 14030.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
240 mMpotassium phosphate1drop
31 mMEDTA1drop
415 mMbeta-mercaptoethanol1drop
510 mMd-equilenin in dimethyl sulfoxide1drop
61.4 Msodium acetate1reservoir
70.1 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 9195 / % possible obs: 93.1 % / Observed criterion σ(I): 0.5 / Redundancy: 8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 13

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Processing

SoftwareName: X-PLOR / Version: 3.81 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 -5 %RANDOM
Rwork0.19 ---
obs0.19 8552 92.8766 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 48 1002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.572
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.81 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.43 Å2

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